FMO DATABASE

FMODB ID: 2J4NR

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	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	46
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-140220.169645
FMO2-HF: Nuclear repulsion	122257.157209
FMO2-HF: Total energy	-17963.012435
FMO2-MP2: Total energy	-18014.193567

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.
-1.324	1.346	-0.02	-1.221	-1.428	-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 : 0.004 / 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

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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	4	17	ASN	0	-0.035	-0.018	3.806	-0.072	2.116	-0.025	-1.118	-1.045	-0.002
4	4	18	THR	0	-0.002	-0.002	3.493	-1.933	-1.516	0.006	-0.103	-0.319	0.000
5	4	19	GLY	0	0.020	0.016	5.030	0.298	0.363	-0.001	0.000	-0.064	0.000
6	4	20	SER	0	-0.037	-0.008	7.965	0.199	0.199	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.040	0.005	9.855	0.010	0.010	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.001	0.020	12.577	0.060	0.060	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.018	0.011	11.435	-0.115	-0.115	0.000	0.000	0.000	0.000
10	4	24	ASN	0	-0.034	-0.045	7.805	0.055	0.055	0.000	0.000	0.000	0.000
11	4	25	TYR	0	-0.039	-0.017	11.737	0.019	0.019	0.000	0.000	0.000	0.000
12	4	26	TYR	0	0.027	0.015	13.643	0.045	0.045	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.013	-0.001	12.892	-0.028	-0.028	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.080	0.040	10.384	-0.006	-0.006	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.042	-0.010	11.318	0.030	0.030	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.063	-0.057	12.538	0.004	0.004	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.020	0.023	7.837	-0.096	-0.096	0.000	0.000	0.000	0.000
18	4	32	ASN	0	0.033	0.012	4.859	-0.477	-0.477	0.000	0.000	0.000	0.000
19	4	33	SER	0	-0.016	-0.012	9.237	-0.028	-0.028	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.010	-0.014	10.527	0.092	0.092	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.888	-0.935	9.107	0.821	0.821	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.058	-0.016	12.256	-0.003	-0.003	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.006	-0.004	15.251	-0.006	-0.006	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.012	-0.004	17.089	-0.035	-0.035	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.020	0.007	20.618	0.011	0.011	0.000	0.000	0.000	0.000
26	4	65	ASN	0	0.014	-0.002	11.217	-0.049	-0.049	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.827	-0.933	12.764	0.335	0.335	0.000	0.000	0.000	0.000
28	4	67	TRP	0	0.066	0.029	14.696	-0.018	-0.018	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.049	0.017	15.781	-0.014	-0.014	0.000	0.000	0.000	0.000
30	4	69	SER	0	0.028	0.027	15.102	0.002	0.002	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.813	0.894	17.041	-0.362	-0.362	0.000	0.000	0.000	0.000
32	4	71	LEU	0	-0.032	-0.005	20.054	-0.017	-0.017	0.000	0.000	0.000	0.000
33	4	72	ALA	0	-0.002	0.022	19.119	-0.016	-0.016	0.000	0.000	0.000	0.000
34	4	73	SER	0	-0.074	-0.039	19.355	-0.003	-0.003	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.035	-0.040	21.908	-0.003	-0.003	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.025	0.035	25.528	-0.011	-0.011	0.000	0.000	0.000	0.000
37	4	76	PHE	0	-0.021	-0.008	27.412	0.003	0.003	0.000	0.000	0.000	0.000
38	4	77	SER	0	0.011	0.004	30.433	-0.005	-0.005	0.000	0.000	0.000	0.000
39	4	78	GLY	0	-0.012	-0.004	32.198	-0.004	-0.004	0.000	0.000	0.000	0.000
40	4	79	LEU	0	0.024	-0.003	35.562	-0.003	-0.003	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.027	-0.008	36.891	0.000	0.000	0.000	0.000	0.000	0.000
42	4	81	GLY	0	0.008	-0.005	41.029	-0.003	-0.003	0.000	0.000	0.000	0.000
43	4	82	ALA	0	0.010	0.001	43.716	0.000	0.000	0.000	0.000	0.000	0.000
44	4	83	LEU	0	-0.034	0.005	40.682	-0.002	-0.002	0.000	0.000	0.000	0.000
45	4	84	LEU	0	0.018	0.009	43.912	-0.001	-0.001	0.000	0.000	0.000	0.000
46	4	85	ALA	0	-0.001	0.005	45.913	0.002	0.002	0.000	0.000	0.000	0.000

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