FMO DATABASE

FMODB ID: 5311Z

Calculation Name: 3ZDM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZDM

Chain ID: B

ChEMBL ID:

UniProt ID: Q12285

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	OptAll
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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-223671.092511
FMO2-HF: Nuclear repulsion	204354.366152
FMO2-HF: Total energy	-19316.726359
FMO2-MP2: Total energy	-19372.073064

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:2:SER)

Summations of interaction energy for fragment #1(B:2: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.
-2.768	-1.642	-0.008	-0.455	-0.664	0.002

Interaction energy analysis for fragmet #1(B:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.038

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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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	4	SER	0	-0.033	-0.056	3.856	1.263	2.389	-0.008	-0.455	-0.664	0.002
4	B	5	LYS	1	0.944	0.943	6.450	1.015	1.015	0.000	0.000	0.000	0.000
5	B	6	GLU	-1	-0.884	-0.918	9.469	-0.708	-0.708	0.000	0.000	0.000	0.000
6	B	7	GLU	-1	-0.786	-0.860	5.713	-4.223	-4.223	0.000	0.000	0.000	0.000
7	B	8	ILE	0	-0.041	-0.023	6.248	0.354	0.354	0.000	0.000	0.000	0.000
8	B	9	ALA	0	0.005	0.006	9.861	0.115	0.115	0.000	0.000	0.000	0.000
9	B	10	ALA	0	0.052	0.027	12.726	0.072	0.072	0.000	0.000	0.000	0.000
10	B	11	LEU	0	-0.016	-0.015	8.889	0.093	0.093	0.000	0.000	0.000	0.000
11	B	12	ILE	0	-0.033	-0.009	13.102	0.058	0.058	0.000	0.000	0.000	0.000
12	B	13	VAL	0	0.029	0.018	15.414	0.015	0.015	0.000	0.000	0.000	0.000
13	B	14	ASN	0	-0.003	0.007	15.922	0.034	0.034	0.000	0.000	0.000	0.000
14	B	15	TYR	0	-0.008	-0.001	16.437	0.021	0.021	0.000	0.000	0.000	0.000
15	B	16	PHE	0	0.034	0.001	18.219	0.007	0.007	0.000	0.000	0.000	0.000
16	B	17	SER	0	0.008	-0.005	20.895	-0.010	-0.010	0.000	0.000	0.000	0.000
17	B	18	SER	0	-0.053	-0.026	20.761	0.011	0.011	0.000	0.000	0.000	0.000
18	B	19	ILE	0	-0.011	-0.010	21.949	0.005	0.005	0.000	0.000	0.000	0.000
19	B	20	VAL	0	-0.017	-0.005	24.497	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	21	GLU	-1	-0.963	-0.991	24.119	-0.012	-0.012	0.000	0.000	0.000	0.000
21	B	22	LYS	1	0.849	0.936	23.224	-0.084	-0.084	0.000	0.000	0.000	0.000
22	B	23	LYS	1	0.826	0.904	28.428	-0.016	-0.016	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.920	-0.964	25.275	0.117	0.117	0.000	0.000	0.000	0.000
24	B	25	ILE	0	-0.070	-0.025	26.945	0.010	0.010	0.000	0.000	0.000	0.000
25	B	26	SER	0	-0.033	-0.035	30.282	-0.005	-0.005	0.000	0.000	0.000	0.000
26	B	27	GLU	-1	-0.832	-0.919	32.016	0.016	0.016	0.000	0.000	0.000	0.000
27	B	28	ASP	-1	-0.795	-0.874	33.016	0.031	0.031	0.000	0.000	0.000	0.000
28	B	29	GLY	0	0.005	0.012	30.685	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	30	ALA	0	0.006	-0.012	28.488	0.002	0.002	0.000	0.000	0.000	0.000
30	B	31	ASP	-1	-0.917	-0.952	28.666	-0.010	-0.010	0.000	0.000	0.000	0.000
31	B	32	SER	0	-0.091	-0.061	29.138	-0.007	-0.007	0.000	0.000	0.000	0.000
32	B	33	LEU	0	-0.010	-0.012	23.383	0.000	0.000	0.000	0.000	0.000	0.000
33	B	34	ASN	0	0.002	0.012	24.651	-0.015	-0.015	0.000	0.000	0.000	0.000
34	B	35	VAL	0	0.061	0.036	25.763	-0.012	-0.012	0.000	0.000	0.000	0.000
35	B	36	ALA	0	-0.008	0.002	23.040	-0.010	-0.010	0.000	0.000	0.000	0.000
36	B	37	MET	0	-0.043	-0.008	20.891	-0.009	-0.009	0.000	0.000	0.000	0.000
37	B	38	ASP	-1	-0.818	-0.882	21.426	-0.106	-0.106	0.000	0.000	0.000	0.000
38	B	39	CYS	0	-0.059	-0.034	22.918	-0.021	-0.021	0.000	0.000	0.000	0.000
39	B	40	ILE	0	-0.060	-0.033	16.988	-0.009	-0.009	0.000	0.000	0.000	0.000
40	B	41	SER	0	-0.004	-0.020	18.107	-0.035	-0.035	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.923	-0.949	19.029	-0.180	-0.180	0.000	0.000	0.000	0.000
42	B	43	ALA	0	-0.072	-0.035	19.026	-0.027	-0.027	0.000	0.000	0.000	0.000
43	B	44	PHE	0	-0.113	-0.073	13.454	0.011	0.011	0.000	0.000	0.000	0.000
44	B	45	GLY	0	-0.025	0.002	15.413	-0.098	-0.098	0.000	0.000	0.000	0.000
45	B	46	PHE	0	-0.037	-0.014	14.719	-0.028	-0.028	0.000	0.000	0.000	0.000
46	B	47	GLU	-1	-0.901	-0.954	19.051	-0.196	-0.196	0.000	0.000	0.000	0.000
47	B	48	ARG	1	0.865	0.905	20.377	0.048	0.048	0.000	0.000	0.000	0.000
48	B	49	GLU	-1	-0.929	-0.979	20.703	-0.167	-0.167	0.000	0.000	0.000	0.000
49	B	50	ALA	0	-0.059	-0.018	18.258	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	51	VAL	0	-0.082	-0.022	15.917	-0.073	-0.073	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:SER)