FMO DATABASE

FMODB ID: 2218R

Calculation Name: 4ZC3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZC3

Chain ID: A

ChEMBL ID:

UniProt ID: P68928

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptHSide
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	57
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-299471.745623
FMO2-HF: Nuclear repulsion	277600.290649
FMO2-HF: Total energy	-21871.454975
FMO2-MP2: Total energy	-21936.004541

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:6:LEU)

Summations of interaction energy for fragment #1(A:6:LEU)

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.
-9.775	-3.551	2.472	-3.079	-5.617	-0.012

Interaction energy analysis for fragmet #1(A:6:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.017

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	A	8	PRO	0	0.106	0.040	3.853	-2.156	-0.668	-0.012	-0.693	-0.783	0.003
4	A	9	LYS	1	0.859	0.941	6.555	-0.209	-0.209	0.000	0.000	0.000	0.000
5	A	10	GLN	0	-0.033	-0.032	3.990	1.306	1.527	0.000	-0.023	-0.198	0.000
6	A	11	GLU	-1	-0.763	-0.847	2.877	-8.383	-5.041	0.405	-1.686	-2.061	-0.017
7	A	12	ARG	1	0.833	0.910	5.914	0.497	0.497	0.000	0.000	0.000	0.000
8	A	13	PHE	0	0.001	-0.006	8.469	0.093	0.093	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.009	0.007	5.176	0.066	0.066	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.797	-0.874	9.270	-0.549	-0.549	0.000	0.000	0.000	0.000
11	A	16	GLU	-1	-0.811	-0.895	11.548	-0.104	-0.104	0.000	0.000	0.000	0.000
12	A	17	TYR	0	-0.019	-0.010	12.426	0.056	0.056	0.000	0.000	0.000	0.000
13	A	18	PHE	0	-0.032	-0.016	11.108	0.019	0.019	0.000	0.000	0.000	0.000
14	A	19	ILE	0	-0.005	0.011	15.109	0.015	0.015	0.000	0.000	0.000	0.000
15	A	20	ASN	0	-0.093	-0.058	17.018	0.032	0.032	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.833	-0.930	19.182	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	22	MET	0	-0.020	-0.007	15.919	0.015	0.015	0.000	0.000	0.000	0.000
18	A	23	ASN	0	0.004	0.019	18.044	0.050	0.050	0.000	0.000	0.000	0.000
19	A	24	ALA	0	0.053	0.004	15.455	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	25	THR	0	0.032	0.010	15.952	0.035	0.035	0.000	0.000	0.000	0.000
21	A	26	LYS	1	0.861	0.937	18.094	0.009	0.009	0.000	0.000	0.000	0.000
22	A	27	ALA	0	0.038	0.037	13.858	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	28	ALA	0	-0.023	-0.014	13.527	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	29	ILE	0	-0.022	-0.021	14.591	0.005	0.005	0.000	0.000	0.000	0.000
25	A	30	ALA	0	-0.015	0.001	16.086	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.008	0.000	11.120	-0.042	-0.042	0.000	0.000	0.000	0.000
27	A	32	GLY	0	0.022	0.019	12.678	0.015	0.015	0.000	0.000	0.000	0.000
28	A	33	TYR	0	-0.053	-0.026	9.194	0.035	0.035	0.000	0.000	0.000	0.000
29	A	34	SER	0	0.028	0.016	15.338	-0.059	-0.059	0.000	0.000	0.000	0.000
30	A	35	LYS	1	1.044	0.995	18.878	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	36	ASN	0	-0.013	-0.005	21.197	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	37	SER	0	0.017	0.015	18.199	0.001	0.001	0.000	0.000	0.000	0.000
33	A	38	ALA	0	-0.012	0.012	17.010	0.038	0.038	0.000	0.000	0.000	0.000
34	A	39	SER	0	0.001	0.000	17.163	0.014	0.014	0.000	0.000	0.000	0.000
35	A	40	ALA	0	0.040	0.018	18.414	0.009	0.009	0.000	0.000	0.000	0.000
36	A	41	ILE	0	0.024	0.007	12.562	0.031	0.031	0.000	0.000	0.000	0.000
37	A	42	GLY	0	0.015	0.008	13.373	0.068	0.068	0.000	0.000	0.000	0.000
38	A	43	ALA	0	-0.015	-0.011	14.053	0.016	0.016	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.868	-0.927	12.263	1.057	1.057	0.000	0.000	0.000	0.000
40	A	45	ASN	0	0.015	-0.011	8.750	0.407	0.407	0.000	0.000	0.000	0.000
41	A	46	LEU	0	-0.024	0.002	10.097	0.054	0.054	0.000	0.000	0.000	0.000
42	A	47	GLN	0	-0.032	-0.019	12.146	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	48	LYS	1	0.870	0.945	7.562	-1.576	-1.576	0.000	0.000	0.000	0.000
44	A	49	PRO	0	0.044	0.026	8.590	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	50	ALA	0	0.000	-0.008	3.241	-0.491	-0.169	0.039	-0.078	-0.283	0.001
46	A	51	ILE	0	-0.023	-0.011	4.808	-0.404	-0.212	-0.001	-0.008	-0.183	0.000
47	A	52	ARG	1	0.874	0.905	6.627	-0.437	-0.437	0.000	0.000	0.000	0.000
48	A	53	ALA	0	0.026	0.018	6.104	-0.131	-0.131	0.000	0.000	0.000	0.000
49	A	54	ARG	1	0.799	0.859	2.314	0.640	1.299	2.041	-0.591	-2.109	0.001
50	A	55	ILE	0	-0.007	0.000	6.671	-0.099	-0.099	0.000	0.000	0.000	0.000
51	A	56	ASP	-1	-0.768	-0.857	10.105	0.042	0.042	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.062	-0.022	8.031	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.869	0.902	9.543	0.472	0.472	0.000	0.000	0.000	0.000
54	A	59	LEU	0	-0.024	-0.017	11.568	0.016	0.016	0.000	0.000	0.000	0.000
55	A	60	LYS	1	0.865	0.933	11.338	0.346	0.346	0.000	0.000	0.000	0.000
56	A	61	GLU	-1	-0.925	-0.962	10.955	-0.455	-0.455	0.000	0.000	0.000	0.000
57	A	62	ILE	0	-0.084	-0.016	15.047	0.023	0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:LEU)