FMO DATABASE

FMODB ID: 9G172

Calculation Name: 3SF4-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SF4

Chain ID: D

ChEMBL ID:

UniProt ID: P81274

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	45
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-152461.790732
FMO2-HF: Nuclear repulsion	133539.46454
FMO2-HF: Total energy	-18922.326192
FMO2-MP2: Total energy	-18972.249983

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(D:24:GLN)

Summations of interaction energy for fragment #1(D:24:GLN)

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.
-3.339	0.932	0.011	-2.113	-2.169	-0.002

Interaction energy analysis for fragmet #1(D:24:GLN)

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 : -0.008

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	D	26	ASP	-1	-0.856	-0.910	3.363	-4.423	-0.311	0.012	-2.106	-2.019	-0.002
4	D	27	SER	0	0.010	-0.005	4.322	0.026	0.185	-0.001	-0.007	-0.150	0.000
5	D	28	VAL	0	-0.007	-0.003	5.067	0.573	0.573	0.000	0.000	0.000	0.000
6	D	29	GLN	0	-0.024	-0.020	7.536	0.435	0.435	0.000	0.000	0.000	0.000
7	D	30	ARG	1	0.828	0.907	9.315	0.997	0.997	0.000	0.000	0.000	0.000
8	D	31	TRP	0	0.046	0.024	10.556	0.111	0.111	0.000	0.000	0.000	0.000
9	D	32	MET	0	-0.006	-0.015	11.525	0.067	0.067	0.000	0.000	0.000	0.000
10	D	33	GLU	-1	-0.907	-0.933	13.519	-0.625	-0.625	0.000	0.000	0.000	0.000
11	D	34	ASP	-1	-0.860	-0.941	15.063	-0.614	-0.614	0.000	0.000	0.000	0.000
12	D	35	LEU	0	-0.019	-0.012	15.915	0.078	0.078	0.000	0.000	0.000	0.000
13	D	36	LYS	1	0.881	0.946	16.523	0.847	0.847	0.000	0.000	0.000	0.000
14	D	37	LEU	0	-0.065	-0.030	19.457	0.072	0.072	0.000	0.000	0.000	0.000
15	D	38	MET	0	-0.031	0.006	18.302	0.034	0.034	0.000	0.000	0.000	0.000
16	D	39	THR	0	-0.026	-0.024	22.464	-0.021	-0.021	0.000	0.000	0.000	0.000
17	D	40	GLU	-1	-0.902	-0.938	24.906	-0.394	-0.394	0.000	0.000	0.000	0.000
18	D	41	CYS	0	-0.100	-0.053	27.694	0.003	0.003	0.000	0.000	0.000	0.000
19	D	42	GLU	-1	-0.874	-0.939	31.244	-0.252	-0.252	0.000	0.000	0.000	0.000
20	D	43	CYS	0	-0.060	-0.007	34.808	0.007	0.007	0.000	0.000	0.000	0.000
21	D	44	MET	0	-0.024	-0.007	34.072	0.005	0.005	0.000	0.000	0.000	0.000
22	D	45	CYS	0	-0.090	-0.055	37.379	0.008	0.008	0.000	0.000	0.000	0.000
23	D	46	VAL	0	0.057	0.031	40.560	0.007	0.007	0.000	0.000	0.000	0.000
24	D	47	LEU	0	-0.054	-0.016	43.440	0.006	0.006	0.000	0.000	0.000	0.000
25	D	48	GLN	0	-0.060	-0.040	46.721	-0.002	-0.002	0.000	0.000	0.000	0.000
26	D	49	ALA	0	-0.035	-0.016	50.362	0.005	0.005	0.000	0.000	0.000	0.000
27	D	50	LYS	1	0.933	0.946	52.685	0.088	0.088	0.000	0.000	0.000	0.000
28	D	51	PRO	0	0.026	0.035	56.454	0.002	0.002	0.000	0.000	0.000	0.000
29	D	52	ILE	0	-0.007	-0.010	58.159	0.002	0.002	0.000	0.000	0.000	0.000
30	D	53	SER	0	-0.038	-0.052	60.564	0.003	0.003	0.000	0.000	0.000	0.000
31	D	54	LEU	0	0.002	-0.008	61.714	-0.002	-0.002	0.000	0.000	0.000	0.000
32	D	55	GLU	-1	-0.887	-0.902	62.010	-0.070	-0.070	0.000	0.000	0.000	0.000
33	D	56	GLU	-1	-0.936	-0.985	61.059	-0.081	-0.081	0.000	0.000	0.000	0.000
34	D	57	ASP	-1	-0.973	-0.978	58.636	-0.090	-0.090	0.000	0.000	0.000	0.000
35	D	58	ALA	0	0.005	0.007	56.084	-0.004	-0.004	0.000	0.000	0.000	0.000
36	D	59	GLN	0	-0.107	-0.052	56.547	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	60	GLY	0	-0.020	-0.006	53.296	-0.003	-0.003	0.000	0.000	0.000	0.000
38	D	61	ASP	-1	-0.868	-0.933	52.133	-0.116	-0.116	0.000	0.000	0.000	0.000
39	D	62	LEU	0	0.012	-0.001	46.901	-0.001	-0.001	0.000	0.000	0.000	0.000
40	D	63	ILE	0	-0.006	0.012	45.160	-0.002	-0.002	0.000	0.000	0.000	0.000
41	D	64	LEU	0	0.012	-0.017	41.386	-0.002	-0.002	0.000	0.000	0.000	0.000
42	D	65	ALA	0	0.006	0.009	41.237	-0.004	-0.004	0.000	0.000	0.000	0.000
43	D	66	GLY	0	0.038	0.016	37.255	-0.011	-0.011	0.000	0.000	0.000	0.000
44	D	67	GLY	0	0.006	0.002	36.769	0.011	0.011	0.000	0.000	0.000	0.000
45	D	68	PRO	0	-0.030	-0.012	32.296	-0.008	-0.008	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:24:GLN)