FMO DATABASE

FMODB ID: 6YVYZ

Calculation Name: 1ZVA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZVA

Chain ID: A

ChEMBL ID:

UniProt ID: Q3I5J5

Base Structure: X-ray

Registration Date: 2023-09-23

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-364975.318755
FMO2-HF: Nuclear repulsion	337792.752415
FMO2-HF: Total energy	-27182.56634
FMO2-MP2: Total energy	-27263.541366

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:ALA)

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

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.
-7.768	-5.066	0.004	-1.128	-1.579	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.010

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	GLY	0	-0.015	-0.016	3.824	-1.590	0.277	-0.004	-0.905	-0.959	0.003
4	A	4	LYS	1	0.962	0.968	3.631	-4.432	-3.814	0.009	-0.172	-0.455	0.001
5	A	5	LEU	0	0.097	0.063	4.283	-0.742	-0.525	-0.001	-0.051	-0.165	0.000
6	A	6	GLN	0	0.014	-0.001	5.849	-0.070	-0.070	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.905	-0.943	8.634	0.443	0.443	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.045	0.029	8.618	-0.084	-0.084	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.020	0.007	9.758	-0.034	-0.034	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.006	-0.001	12.080	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.020	-0.007	13.895	-0.075	-0.075	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.012	-0.015	13.395	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.018	0.024	15.948	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.043	-0.021	17.831	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.011	0.010	19.287	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.033	0.016	19.496	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.013	-0.010	21.670	0.005	0.005	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.023	-0.015	23.798	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.029	0.017	22.815	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.017	0.014	25.085	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.880	0.944	26.913	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.022	-0.013	28.748	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.081	0.037	28.686	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.076	-0.035	31.156	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.064	-0.023	33.474	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	ASN	0	0.036	0.010	33.760	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.039	0.009	35.110	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.018	0.026	37.019	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.005	0.000	39.327	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.000	-0.011	38.120	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.052	-0.032	39.935	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.008	0.015	41.882	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.050	0.020	44.480	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.003	-0.006	42.159	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.040	-0.014	45.808	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.938	-0.954	47.341	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.044	-0.030	48.202	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.034	-0.022	48.065	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.025	0.005	50.635	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.049	-0.025	52.938	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.888	0.943	53.582	0.006	0.006	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.006	0.011	54.483	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.055	0.001	50.754	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.850	-0.869	50.330	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.014	-0.011	47.724	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.017	-0.048	47.260	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.034	-0.014	44.775	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.025	0.012	42.623	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	ASN	0	0.011	-0.005	41.671	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.005	-0.004	40.275	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.030	0.021	38.045	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.005	0.008	36.820	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.031	-0.015	36.025	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.087	-0.045	33.901	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.061	0.032	32.214	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.015	-0.007	31.443	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.936	0.973	30.109	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.853	-0.956	27.828	0.006	0.006	0.000	0.000	0.000	0.000
59	A	59	ILE	0	0.016	0.011	26.620	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.878	-0.931	26.043	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.884	0.929	23.840	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.003	-0.004	22.170	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.021	-0.002	21.309	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.937	-0.971	20.094	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.045	-0.008	17.186	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.003	-0.004	16.388	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.942	0.977	16.102	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	68	ASN	0	0.007	0.002	13.796	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.032	-0.021	11.909	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.002	0.015	11.128	-0.111	-0.111	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.905	-0.961	11.341	-0.111	-0.111	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.114	-0.060	7.589	-0.074	-0.074	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.047	-0.031	6.256	-0.271	-0.271	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.080	-0.025	7.674	-0.124	-0.124	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.988	-0.983	8.200	-0.193	-0.193	0.000	0.000	0.000	0.000

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