FMO DATABASE

FMODB ID: 72Y6K

Calculation Name: 5DDJ-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DDJ

Chain ID: 4

ChEMBL ID:

UniProt ID: Q6PMW3

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	46
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-140320.780582
FMO2-HF: Nuclear repulsion	122358.243792
FMO2-HF: Total energy	-17962.536791
FMO2-MP2: Total energy	-18013.803561

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.
-1.161	1.523	-0.02	-1.246	-1.418	-0.002

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 : 0.002 / q_NPA : -0.016

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	4	17	ASN	0	-0.020	-0.010	3.806	-0.247	2.003	-0.026	-1.177	-1.047	-0.002
4	4	18	THR	0	-0.002	0.001	3.352	-1.677	-1.304	0.007	-0.069	-0.311	0.000
5	4	19	GLY	0	0.013	0.010	5.073	0.222	0.283	-0.001	0.000	-0.060	0.000
6	4	20	SER	0	-0.025	-0.001	7.980	0.151	0.151	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.038	0.009	9.851	-0.011	-0.011	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.003	0.022	12.573	0.038	0.038	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.031	0.013	11.402	-0.129	-0.129	0.000	0.000	0.000	0.000
10	4	24	ASN	0	-0.055	-0.064	7.835	0.016	0.016	0.000	0.000	0.000	0.000
11	4	25	TYR	0	-0.021	-0.011	11.864	0.024	0.024	0.000	0.000	0.000	0.000
12	4	26	TYR	0	0.013	0.011	13.611	0.035	0.035	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.013	-0.003	13.241	-0.032	-0.032	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.077	0.040	10.577	0.026	0.026	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.042	-0.017	11.471	0.032	0.032	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.076	-0.064	12.721	0.017	0.017	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.011	0.029	7.613	-0.004	-0.004	0.000	0.000	0.000	0.000
18	4	32	ASN	0	0.037	0.012	5.100	-0.353	-0.353	0.000	0.000	0.000	0.000
19	4	33	SER	0	-0.022	-0.014	9.280	-0.051	-0.051	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.002	-0.005	10.251	0.099	0.099	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.889	-0.931	9.066	0.840	0.840	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.057	-0.026	12.083	-0.023	-0.023	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.010	0.003	15.096	0.003	0.003	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.022	0.001	16.889	-0.026	-0.026	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.027	0.004	20.389	0.006	0.006	0.000	0.000	0.000	0.000
26	4	65	ASN	0	-0.041	-0.025	11.626	-0.042	-0.042	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.872	-0.952	12.761	0.321	0.321	0.000	0.000	0.000	0.000
28	4	67	TRP	0	0.046	0.008	14.694	-0.026	-0.026	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.042	0.013	15.808	-0.017	-0.017	0.000	0.000	0.000	0.000
30	4	69	SER	0	0.014	0.016	14.944	-0.022	-0.022	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.953	0.968	17.049	-0.269	-0.269	0.000	0.000	0.000	0.000
32	4	71	LEU	0	-0.034	-0.008	20.061	-0.017	-0.017	0.000	0.000	0.000	0.000
33	4	72	ALA	0	-0.006	0.029	19.137	-0.014	-0.014	0.000	0.000	0.000	0.000
34	4	73	SER	0	-0.053	-0.035	19.306	-0.008	-0.008	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.056	-0.048	21.924	-0.004	-0.004	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.036	0.042	25.542	-0.008	-0.008	0.000	0.000	0.000	0.000
37	4	76	PHE	0	-0.026	-0.011	27.426	0.002	0.002	0.000	0.000	0.000	0.000
38	4	77	SER	0	0.012	0.005	30.493	-0.003	-0.003	0.000	0.000	0.000	0.000
39	4	78	GLY	0	-0.016	-0.007	32.217	-0.004	-0.004	0.000	0.000	0.000	0.000
40	4	79	LEU	0	0.022	0.002	35.581	-0.002	-0.002	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.016	-0.006	37.492	0.000	0.000	0.000	0.000	0.000	0.000
42	4	81	GLY	0	0.000	-0.010	41.043	-0.003	-0.003	0.000	0.000	0.000	0.000
43	4	82	ALA	0	-0.001	-0.005	43.764	0.000	0.000	0.000	0.000	0.000	0.000
44	4	83	LEU	0	-0.008	0.014	40.744	-0.002	-0.002	0.000	0.000	0.000	0.000
45	4	84	LEU	0	0.011	0.014	43.934	-0.001	-0.001	0.000	0.000	0.000	0.000
46	4	85	ALA	0	-0.009	-0.005	45.938	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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