FMO DATABASE

FMODB ID: 17NLZ

Calculation Name: 1ZBE-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZBE

Chain ID: 4

ChEMBL ID:

UniProt ID: P03306

Base Structure: X-ray

Registration Date: 2023-06-22

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-157655.167334
FMO2-HF: Nuclear repulsion	138539.505678
FMO2-HF: Total energy	-19115.661656
FMO2-MP2: Total energy	-19170.256049

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(4:15:SER)

Summations of interaction energy for fragment #1(4:15:SER)

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.
-1.37	2.455	2.157	-2.787	-3.194	0.016

Interaction energy analysis for fragmet #1(4:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.014

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

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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	4	17	ASN	0	-0.053	-0.026	3.636	1.469	3.957	0.020	-1.306	-1.203	0.006
4	4	18	THR	0	0.029	0.012	2.094	-2.121	-0.869	2.138	-1.448	-1.941	0.010
5	4	19	GLY	0	0.001	-0.001	4.235	-0.680	-0.595	-0.001	-0.033	-0.050	0.000
6	4	20	SER	0	-0.036	-0.007	6.325	0.157	0.157	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.037	0.021	7.969	-0.072	-0.072	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.029	-0.015	10.437	0.065	0.065	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.009	0.007	10.060	-0.052	-0.052	0.000	0.000	0.000	0.000
10	4	24	ASN	0	0.005	0.000	8.356	0.040	0.040	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.006	0.007	10.835	0.043	0.043	0.000	0.000	0.000	0.000
12	4	26	TYR	0	0.003	0.011	13.003	0.018	0.018	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.014	0.001	12.847	0.014	0.014	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.063	0.007	9.653	0.103	0.103	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.025	-0.022	12.241	0.028	0.028	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.027	0.003	14.226	-0.022	-0.022	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.031	-0.002	8.605	-0.084	-0.084	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.025	-0.018	7.427	-0.020	-0.020	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.024	0.024	11.183	-0.051	-0.051	0.000	0.000	0.000	0.000
20	4	34	MET	0	0.007	0.000	12.406	0.098	0.098	0.000	0.000	0.000	0.000
21	4	35	SER	0	-0.002	0.003	11.594	-0.055	-0.055	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.010	-0.004	14.109	-0.022	-0.022	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.013	-0.016	14.881	0.069	0.069	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.032	0.018	18.926	-0.013	-0.013	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.019	-0.002	21.997	-0.009	-0.009	0.000	0.000	0.000	0.000
26	4	62	THR	0	0.043	0.028	7.828	0.022	0.022	0.000	0.000	0.000	0.000
27	4	63	GLN	0	0.007	-0.018	10.889	0.030	0.030	0.000	0.000	0.000	0.000
28	4	64	ASN	0	0.009	0.012	12.122	-0.047	-0.047	0.000	0.000	0.000	0.000
29	4	65	ASN	0	-0.070	-0.042	13.605	-0.042	-0.042	0.000	0.000	0.000	0.000
30	4	66	ASP	-1	-0.787	-0.900	11.807	-0.277	-0.277	0.000	0.000	0.000	0.000
31	4	67	TRP	0	-0.041	-0.028	14.633	-0.013	-0.013	0.000	0.000	0.000	0.000
32	4	68	PHE	0	0.080	0.014	16.466	-0.002	-0.002	0.000	0.000	0.000	0.000
33	4	69	SER	0	0.036	0.065	14.091	-0.001	-0.001	0.000	0.000	0.000	0.000
34	4	70	LYS	1	0.913	0.957	16.206	0.035	0.035	0.000	0.000	0.000	0.000
35	4	71	LEU	0	-0.005	-0.011	19.116	0.002	0.002	0.000	0.000	0.000	0.000
36	4	72	ALA	0	0.004	0.016	18.808	0.007	0.007	0.000	0.000	0.000	0.000
37	4	73	SER	0	-0.045	-0.036	18.609	-0.006	-0.006	0.000	0.000	0.000	0.000
38	4	74	SER	0	-0.115	-0.061	21.057	0.014	0.014	0.000	0.000	0.000	0.000
39	4	75	ALA	0	0.002	0.014	24.029	0.013	0.013	0.000	0.000	0.000	0.000
40	4	76	PHE	0	-0.019	-0.014	26.030	-0.002	-0.002	0.000	0.000	0.000	0.000
41	4	77	THR	0	0.007	-0.006	27.077	-0.007	-0.007	0.000	0.000	0.000	0.000
42	4	78	GLY	0	-0.051	-0.022	29.459	0.000	0.000	0.000	0.000	0.000	0.000
43	4	79	LEU	0	0.042	0.026	32.908	-0.002	-0.002	0.000	0.000	0.000	0.000
44	4	80	PHE	0	0.007	-0.004	36.280	0.002	0.002	0.000	0.000	0.000	0.000
45	4	81	GLY	0	-0.005	0.003	38.544	0.001	0.001	0.000	0.000	0.000	0.000
46	4	82	ALA	0	-0.017	-0.001	41.653	-0.001	-0.001	0.000	0.000	0.000	0.000
47	4	83	LEU	0	0.003	-0.004	40.281	-0.001	-0.001	0.000	0.000	0.000	0.000
48	4	84	LEU	0	0.004	-0.008	43.373	0.002	0.002	0.000	0.000	0.000	0.000
49	4	85	ALA	0	-0.002	0.017	42.329	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(4:15:SER)