FMO DATABASE

FMODB ID: YV6V2

Calculation Name: 1ZW0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZW0

Chain ID: B

ChEMBL ID:

UniProt ID: O68692

Base Structure: X-ray

Registration Date: 2023-09-20

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	59
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-301051.587107
FMO2-HF: Nuclear repulsion	276000.517557
FMO2-HF: Total energy	-25051.06955
FMO2-MP2: Total energy	-25121.053668

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-14.608	-8.196	1.045	-3.239	-4.217	-0.016

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / 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

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	B	3	GLN	0	0.049	0.024	3.774	-2.687	-1.187	-0.002	-0.634	-0.863	0.002
4	B	4	LEU	0	0.011	0.011	2.464	-1.102	-0.086	0.800	-0.539	-1.277	-0.001
5	B	5	GLU	-1	-0.926	-0.968	3.033	-12.525	-8.629	0.247	-2.066	-2.077	-0.017
6	B	6	GLU	-1	-0.972	-0.979	5.593	0.130	0.130	0.000	0.000	0.000	0.000
7	B	7	GLN	0	0.005	-0.016	7.039	0.263	0.263	0.000	0.000	0.000	0.000
8	B	8	LEU	0	-0.022	-0.021	6.383	0.270	0.270	0.000	0.000	0.000	0.000
9	B	9	HIS	0	0.012	0.017	9.496	0.155	0.155	0.000	0.000	0.000	0.000
10	B	10	ASN	0	-0.013	-0.003	11.510	0.191	0.191	0.000	0.000	0.000	0.000
11	B	11	VAL	0	0.002	0.007	12.839	0.124	0.124	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.854	-0.943	13.529	-0.669	-0.669	0.000	0.000	0.000	0.000
13	B	13	THR	0	-0.014	-0.005	15.268	0.114	0.114	0.000	0.000	0.000	0.000
14	B	14	VAL	0	0.001	0.009	17.431	0.076	0.076	0.000	0.000	0.000	0.000
15	B	15	ARG	1	0.885	0.955	17.329	0.687	0.687	0.000	0.000	0.000	0.000
16	B	16	SER	0	-0.026	-0.001	19.210	0.076	0.076	0.000	0.000	0.000	0.000
17	B	17	ILE	0	0.013	-0.011	20.987	0.047	0.047	0.000	0.000	0.000	0.000
18	B	18	THR	0	-0.018	-0.010	22.879	0.048	0.048	0.000	0.000	0.000	0.000
19	B	19	MET	0	0.020	0.008	21.204	0.030	0.030	0.000	0.000	0.000	0.000
20	B	20	GLN	0	-0.047	-0.021	22.982	0.052	0.052	0.000	0.000	0.000	0.000
21	B	21	LEU	0	-0.003	0.006	27.191	0.027	0.027	0.000	0.000	0.000	0.000
22	B	22	GLU	-1	-0.836	-0.932	27.287	-0.267	-0.267	0.000	0.000	0.000	0.000
23	B	23	MET	0	-0.013	-0.004	29.195	0.015	0.015	0.000	0.000	0.000	0.000
24	B	24	ALA	0	-0.030	-0.009	31.461	0.018	0.018	0.000	0.000	0.000	0.000
25	B	25	LEU	0	0.023	0.007	32.473	0.017	0.017	0.000	0.000	0.000	0.000
26	B	26	THR	0	-0.014	-0.018	33.959	0.016	0.016	0.000	0.000	0.000	0.000
27	B	27	LYS	1	0.867	0.938	35.858	0.169	0.169	0.000	0.000	0.000	0.000
28	B	28	LEU	0	0.011	0.010	37.491	0.009	0.009	0.000	0.000	0.000	0.000
29	B	29	LYS	1	0.889	0.934	38.521	0.159	0.159	0.000	0.000	0.000	0.000
30	B	30	LYS	1	0.911	0.950	40.007	0.147	0.147	0.000	0.000	0.000	0.000
31	B	31	ASP	-1	-0.935	-0.971	41.369	-0.137	-0.137	0.000	0.000	0.000	0.000
32	B	32	MET	0	-0.061	-0.007	42.323	0.008	0.008	0.000	0.000	0.000	0.000
33	B	33	MET	0	-0.106	-0.032	45.104	0.010	0.010	0.000	0.000	0.000	0.000
34	B	41	TYR	0	0.087	0.030	50.285	0.001	0.001	0.000	0.000	0.000	0.000
35	B	42	GLN	0	0.014	-0.003	51.810	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	43	VAL	0	0.051	0.020	49.485	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	44	TRP	0	0.074	0.039	46.731	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	45	GLN	0	0.010	0.002	46.855	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	46	ARG	1	0.881	0.937	46.506	0.079	0.079	0.000	0.000	0.000	0.000
40	B	47	GLU	-1	-0.878	-0.936	42.691	-0.122	-0.122	0.000	0.000	0.000	0.000
41	B	48	SER	0	0.041	0.015	42.487	-0.009	-0.009	0.000	0.000	0.000	0.000
42	B	49	LYS	1	0.950	0.969	41.598	0.104	0.104	0.000	0.000	0.000	0.000
43	B	50	ALA	0	0.016	0.014	41.080	-0.005	-0.005	0.000	0.000	0.000	0.000
44	B	51	LEU	0	0.018	0.006	37.791	-0.008	-0.008	0.000	0.000	0.000	0.000
45	B	52	GLU	-1	-0.879	-0.929	36.829	-0.147	-0.147	0.000	0.000	0.000	0.000
46	B	53	SER	0	-0.034	-0.019	36.435	-0.007	-0.007	0.000	0.000	0.000	0.000
47	B	54	ALA	0	-0.012	0.003	34.868	-0.006	-0.006	0.000	0.000	0.000	0.000
48	B	55	ILE	0	-0.008	-0.008	32.025	-0.012	-0.012	0.000	0.000	0.000	0.000
49	B	56	ALA	0	-0.004	-0.009	31.500	-0.014	-0.014	0.000	0.000	0.000	0.000
50	B	57	ILE	0	-0.025	-0.011	31.371	-0.010	-0.010	0.000	0.000	0.000	0.000
51	B	58	ILE	0	0.010	0.008	27.202	-0.009	-0.009	0.000	0.000	0.000	0.000
52	B	59	HIS	0	-0.033	-0.009	27.020	-0.017	-0.017	0.000	0.000	0.000	0.000
53	B	60	TYR	0	-0.071	-0.034	26.677	-0.016	-0.016	0.000	0.000	0.000	0.000
54	B	61	VAL	0	0.014	0.008	25.549	-0.010	-0.010	0.000	0.000	0.000	0.000
55	B	62	ALA	0	-0.008	-0.007	22.948	-0.019	-0.019	0.000	0.000	0.000	0.000
56	B	63	GLY	0	0.012	0.012	21.918	-0.043	-0.043	0.000	0.000	0.000	0.000
57	B	64	ASP	-1	-0.914	-0.956	21.702	-0.316	-0.316	0.000	0.000	0.000	0.000
58	B	65	LEU	0	-0.087	-0.037	18.187	-0.030	-0.030	0.000	0.000	0.000	0.000
59	B	66	LYS	1	0.878	0.940	15.999	0.551	0.551	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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