FMO DATABASE

FMODB ID: 2KZVR

Calculation Name: 1Z0P-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z0P

Chain ID: A

ChEMBL ID:

UniProt ID: Q99YR7

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	78
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-474069.197957
FMO2-HF: Nuclear repulsion	442132.295144
FMO2-HF: Total energy	-31936.902813
FMO2-MP2: Total energy	-32030.40693

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:MET )

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

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.
-18.574	-12.067	5.115	-2.96	-8.662	-0.015

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.025

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	TYR	0	0.098	0.036	3.068	-3.681	-1.466	0.140	-1.175	-1.180	-0.001
4	A	4	GLU	-1	-0.889	-0.955	5.745	-0.677	-0.677	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.890	0.948	2.265	-5.059	-3.690	1.650	-0.755	-2.264	0.003
6	A	6	GLU	-1	-0.911	-0.958	2.374	-8.865	-6.436	2.666	-1.474	-3.621	-0.014
7	A	7	PHE	0	0.014	0.024	3.301	1.035	0.568	0.064	0.729	-0.326	-0.001
8	A	8	LEU	0	-0.023	-0.030	6.755	0.224	0.224	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.884	0.953	2.353	0.031	0.992	0.595	-0.285	-1.271	-0.002
10	A	10	ASP	-1	-0.857	-0.927	5.386	-2.960	-2.960	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.089	-0.041	6.970	0.275	0.275	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.824	-0.919	8.788	0.895	0.895	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.866	-0.943	7.132	-0.422	-0.422	0.000	0.000	0.000	0.000
14	A	14	TRP	0	-0.016	-0.007	10.268	0.041	0.041	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.010	0.002	12.667	0.034	0.034	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.944	0.974	10.934	-0.359	-0.359	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.003	0.012	13.686	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.039	-0.022	16.124	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.023	0.040	17.676	0.004	0.004	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.013	-0.001	17.015	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.052	-0.025	19.944	0.001	0.001	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.066	-0.078	21.954	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.064	0.037	22.916	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.015	0.025	25.046	0.005	0.005	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.001	0.010	26.629	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.026	0.001	28.049	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.018	0.003	29.371	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.029	-0.021	30.396	0.000	0.000	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.067	-0.043	32.367	0.003	0.003	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.006	-0.012	33.827	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.943	-0.955	35.327	-0.022	-0.022	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.032	-0.020	37.209	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.037	0.031	38.509	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	GLN	0	-0.202	-0.113	39.550	0.010	0.010	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-1.016	-0.982	41.373	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.854	-0.940	43.460	-0.042	-0.042	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.024	0.006	42.681	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.977	-1.011	43.113	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.940	-0.975	41.555	-0.043	-0.043	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.942	0.973	38.898	0.068	0.068	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.066	0.042	37.274	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	42	LYS	1	1.029	1.015	36.482	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.862	-0.938	36.398	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.131	-0.084	33.304	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.030	0.026	32.034	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.028	0.012	31.722	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.881	0.959	29.431	0.079	0.079	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.051	-0.049	27.446	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.867	-0.951	26.913	0.011	0.011	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.003	0.018	27.777	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.879	0.929	23.841	0.109	0.109	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.018	-0.002	22.447	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.874	-0.921	23.118	0.063	0.063	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.002	0.001	23.014	0.018	0.018	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.058	-0.058	18.489	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.854	-0.940	18.945	0.134	0.134	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.017	0.001	20.411	0.047	0.047	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.061	-0.045	16.728	0.037	0.037	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.016	0.006	14.605	0.055	0.055	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.068	0.043	16.172	0.076	0.076	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.811	0.909	16.529	-0.185	-0.185	0.000	0.000	0.000	0.000
62	A	62	PHE	0	0.017	0.002	10.799	0.070	0.070	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.842	-0.924	12.445	0.760	0.760	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.069	-0.032	14.806	0.097	0.097	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.013	-0.002	6.102	-0.115	-0.115	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.781	0.899	9.444	-0.669	-0.669	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.069	-0.050	11.402	0.048	0.048	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.057	-0.017	13.177	-0.043	-0.043	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.852	0.942	14.103	-0.547	-0.547	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.006	0.011	16.213	0.022	0.022	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.059	0.008	16.392	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	72	HIS	0	-0.047	-0.053	18.382	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.856	-0.901	20.470	0.332	0.332	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.014	0.006	21.566	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.026	-0.013	19.704	0.020	0.020	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.885	-0.931	20.543	0.413	0.413	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.951	-0.976	21.863	0.204	0.204	0.000	0.000	0.000	0.000
78	A	78	NME	0	-0.045	-0.021	24.408	0.009	0.009	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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