FMO DATABASE

FMODB ID: ZV8ZN

Calculation Name: 3NZL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NZL

Chain ID: A

ChEMBL ID:

UniProt ID: Q01826

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-469789.01852
FMO2-HF: Nuclear repulsion	439445.007266
FMO2-HF: Total energy	-30344.011254
FMO2-MP2: Total energy	-30429.93601

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:7:HIS)

Summations of interaction energy for fragment #1(A:7:HIS)

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.
-39.376	-43.85	24.007	-8.567	-10.964	0.061

Interaction energy analysis for fragmet #1(A:7:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.105 / q_NPA : 0.061

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	9	SER	0	-0.028	-0.046	1.863	-25.394	-32.692	23.737	-8.207	-8.232	0.061
4	A	10	HIS	0	-0.017	-0.018	3.139	-8.765	-6.227	0.271	-0.329	-2.479	0.000
5	A	11	MET	0	-0.032	0.012	4.634	-1.444	-1.158	-0.001	-0.031	-0.253	0.000
6	A	12	LEU	0	0.032	0.013	6.925	0.217	0.217	0.000	0.000	0.000	0.000
7	A	13	PRO	0	0.027	0.034	10.432	0.152	0.152	0.000	0.000	0.000	0.000
8	A	14	PRO	0	0.015	-0.015	12.404	-0.115	-0.115	0.000	0.000	0.000	0.000
9	A	15	GLU	-1	-0.875	-0.952	15.383	0.751	0.751	0.000	0.000	0.000	0.000
10	A	16	GLN	0	-0.008	0.000	14.344	-0.075	-0.075	0.000	0.000	0.000	0.000
11	A	17	TRP	0	-0.097	-0.022	11.105	-0.078	-0.078	0.000	0.000	0.000	0.000
12	A	18	SER	0	0.046	0.013	16.579	-0.089	-0.089	0.000	0.000	0.000	0.000
13	A	19	HIS	0	0.090	0.015	18.740	0.060	0.060	0.000	0.000	0.000	0.000
14	A	20	THR	0	-0.005	0.000	17.807	0.000	0.000	0.000	0.000	0.000	0.000
15	A	21	THR	0	0.023	0.017	13.472	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	22	VAL	0	0.027	0.022	15.300	0.075	0.075	0.000	0.000	0.000	0.000
17	A	23	ARG	1	0.944	0.978	17.446	-0.414	-0.414	0.000	0.000	0.000	0.000
18	A	24	ASN	0	-0.029	-0.022	14.807	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	25	ALA	0	0.015	0.015	13.204	0.040	0.040	0.000	0.000	0.000	0.000
20	A	26	LEU	0	0.001	0.004	14.238	0.013	0.013	0.000	0.000	0.000	0.000
21	A	27	LYS	1	0.932	0.947	17.552	-0.536	-0.536	0.000	0.000	0.000	0.000
22	A	28	ASP	-1	-0.953	-0.966	12.130	1.247	1.247	0.000	0.000	0.000	0.000
23	A	29	LEU	0	0.015	0.002	13.378	0.003	0.003	0.000	0.000	0.000	0.000
24	A	30	LEU	0	-0.060	-0.034	16.040	-0.064	-0.064	0.000	0.000	0.000	0.000
25	A	31	LYS	1	0.895	0.962	16.438	-0.736	-0.736	0.000	0.000	0.000	0.000
26	A	32	ASP	-1	-0.875	-0.914	15.283	0.703	0.703	0.000	0.000	0.000	0.000
27	A	33	MET	0	-0.068	-0.023	15.849	-0.055	-0.055	0.000	0.000	0.000	0.000
28	A	34	ASN	0	0.057	0.032	20.308	0.011	0.011	0.000	0.000	0.000	0.000
29	A	35	GLN	0	0.087	0.002	22.865	0.012	0.012	0.000	0.000	0.000	0.000
30	A	36	SER	0	-0.038	-0.005	24.654	0.008	0.008	0.000	0.000	0.000	0.000
31	A	37	SER	0	0.041	0.003	21.672	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.033	0.015	18.254	0.013	0.013	0.000	0.000	0.000	0.000
33	A	39	ALA	0	-0.034	-0.025	21.095	0.015	0.015	0.000	0.000	0.000	0.000
34	A	40	LYS	1	0.858	0.940	23.491	-0.250	-0.250	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.898	-0.936	18.089	0.440	0.440	0.000	0.000	0.000	0.000
36	A	42	CYS	0	-0.083	0.000	18.502	0.024	0.024	0.000	0.000	0.000	0.000
37	A	43	PRO	0	0.033	0.012	19.081	-0.045	-0.045	0.000	0.000	0.000	0.000
38	A	44	LEU	0	-0.049	-0.028	20.425	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	45	SER	0	0.056	0.028	23.677	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	46	GLN	0	0.084	0.017	26.601	0.009	0.009	0.000	0.000	0.000	0.000
41	A	47	SER	0	-0.003	0.007	28.417	0.009	0.009	0.000	0.000	0.000	0.000
42	A	48	MET	0	-0.006	0.002	24.829	0.011	0.011	0.000	0.000	0.000	0.000
43	A	49	ILE	0	0.019	0.007	22.878	0.015	0.015	0.000	0.000	0.000	0.000
44	A	50	SER	0	0.024	0.017	25.248	0.009	0.009	0.000	0.000	0.000	0.000
45	A	51	SER	0	0.014	0.007	28.279	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	52	ILE	0	-0.052	-0.028	21.947	0.001	0.001	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.068	-0.036	23.984	0.008	0.008	0.000	0.000	0.000	0.000
48	A	54	ASN	0	-0.028	-0.023	25.816	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.024	0.013	28.932	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	56	THR	0	0.035	0.013	29.076	0.012	0.012	0.000	0.000	0.000	0.000
51	A	57	TYR	0	-0.038	-0.012	30.511	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	58	TYR	0	-0.041	-0.018	26.452	0.017	0.017	0.000	0.000	0.000	0.000
53	A	59	ALA	0	0.012	0.006	24.342	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	60	ASN	0	0.018	0.007	26.142	0.006	0.006	0.000	0.000	0.000	0.000
55	A	61	VAL	0	0.000	-0.013	22.233	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	62	SER	0	0.031	0.018	25.105	0.014	0.014	0.000	0.000	0.000	0.000
57	A	63	ALA	0	0.118	0.043	23.315	0.031	0.031	0.000	0.000	0.000	0.000
58	A	64	ALA	0	0.021	0.011	22.475	0.040	0.040	0.000	0.000	0.000	0.000
59	A	65	LYS	1	0.835	0.910	22.319	-0.360	-0.360	0.000	0.000	0.000	0.000
60	A	66	CYS	0	-0.026	-0.007	19.427	0.045	0.045	0.000	0.000	0.000	0.000
61	A	67	GLN	0	-0.004	0.004	18.141	0.085	0.085	0.000	0.000	0.000	0.000
62	A	68	GLU	-1	-0.870	-0.929	17.385	0.487	0.487	0.000	0.000	0.000	0.000
63	A	69	PHE	0	0.020	-0.005	15.069	0.045	0.045	0.000	0.000	0.000	0.000
64	A	70	GLY	0	0.043	0.006	14.188	0.092	0.092	0.000	0.000	0.000	0.000
65	A	71	ARG	1	0.908	0.950	12.998	-0.421	-0.421	0.000	0.000	0.000	0.000
66	A	72	TRP	0	0.041	0.025	12.781	0.159	0.159	0.000	0.000	0.000	0.000
67	A	73	TYR	0	0.039	0.014	9.145	0.066	0.066	0.000	0.000	0.000	0.000
68	A	74	LYS	1	0.848	0.924	6.491	-3.301	-3.301	0.000	0.000	0.000	0.000
69	A	75	HIS	0	-0.030	-0.016	8.476	0.392	0.392	0.000	0.000	0.000	0.000
70	A	76	PHE	0	0.020	0.010	10.296	-0.076	-0.076	0.000	0.000	0.000	0.000
71	A	77	LYS	1	0.949	0.967	6.566	-2.070	-2.070	0.000	0.000	0.000	0.000
72	A	78	LYS	1	0.869	0.953	5.714	0.545	0.545	0.000	0.000	0.000	0.000
73	A	79	THR	0	-0.035	-0.005	7.225	-0.783	-0.783	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:7:HIS)