FMO DATABASE

FMODB ID: 52RGZ

Calculation Name: 5NE4-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NE4

Chain ID: 4

ChEMBL ID:

UniProt ID: Q7TD07

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

Total energy (hartree)

FMO2-HF: Electronic energy	-140309.636277
FMO2-HF: Nuclear repulsion	122327.048299
FMO2-HF: Total energy	-17982.587978
FMO2-MP2: Total energy	-18033.743429

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.
-2.448	0.085	0.153	-1.189	-1.498	0.003

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 : 0.035 / q_NPA : 0.013

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	4	17	ASN	0	-0.025	-0.012	3.810	-2.205	-0.434	-0.020	-0.890	-0.861	0.003
4	4	18	THR	0	-0.016	-0.021	2.627	-0.340	0.353	0.174	-0.288	-0.580	0.000
5	4	19	GLY	0	0.040	0.018	4.470	-0.464	-0.395	-0.001	-0.011	-0.057	0.000
6	4	20	SER	0	-0.028	0.000	6.815	0.070	0.070	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.029	0.008	7.997	0.129	0.129	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.054	-0.012	10.553	0.038	0.038	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.022	-0.001	10.360	0.138	0.138	0.000	0.000	0.000	0.000
10	4	24	ASN	0	-0.028	-0.020	9.643	-0.115	-0.115	0.000	0.000	0.000	0.000
11	4	25	TYR	0	-0.011	-0.003	11.561	-0.012	-0.012	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.001	0.010	13.835	-0.020	-0.020	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.037	0.007	13.293	0.044	0.044	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.076	0.028	7.885	-0.018	-0.018	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.020	-0.018	11.394	0.003	0.003	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.045	-0.021	13.794	-0.019	-0.019	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.014	0.014	9.289	-0.027	-0.027	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.040	-0.028	7.176	0.004	0.004	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.045	0.037	10.170	-0.035	-0.035	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.030	-0.024	10.499	0.053	0.053	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.904	-0.936	9.405	0.599	0.599	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.049	-0.032	12.721	-0.043	-0.043	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.007	-0.003	14.153	0.039	0.039	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.010	0.004	17.645	-0.015	-0.015	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.012	-0.002	20.981	-0.004	-0.004	0.000	0.000	0.000	0.000
26	4	65	ASP	-1	-0.911	-0.967	10.118	-0.245	-0.245	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.784	-0.915	11.918	0.088	0.088	0.000	0.000	0.000	0.000
28	4	67	TRP	0	-0.004	-0.003	14.261	-0.027	-0.027	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.061	0.012	16.059	-0.011	-0.011	0.000	0.000	0.000	0.000
30	4	69	SER	0	0.008	0.042	14.080	-0.015	-0.015	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.823	0.909	16.173	-0.032	-0.032	0.000	0.000	0.000	0.000
32	4	71	LEU	0	-0.015	0.003	19.079	-0.002	-0.002	0.000	0.000	0.000	0.000
33	4	72	ALA	0	0.000	0.001	18.811	0.000	0.000	0.000	0.000	0.000	0.000
34	4	73	SER	0	-0.037	-0.033	18.546	-0.009	-0.009	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.108	-0.047	21.196	0.006	0.006	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.002	0.012	24.121	0.007	0.007	0.000	0.000	0.000	0.000
37	4	76	PHE	0	-0.007	-0.006	26.105	-0.002	-0.002	0.000	0.000	0.000	0.000
38	4	77	SER	0	-0.021	-0.017	27.550	-0.005	-0.005	0.000	0.000	0.000	0.000
39	4	78	GLY	0	0.012	0.011	30.119	-0.003	-0.003	0.000	0.000	0.000	0.000
40	4	79	LEU	0	-0.012	-0.008	33.735	0.000	0.000	0.000	0.000	0.000	0.000
41	4	80	PHE	0	0.003	-0.004	37.243	0.001	0.001	0.000	0.000	0.000	0.000
42	4	81	GLY	0	-0.003	0.004	38.894	0.002	0.002	0.000	0.000	0.000	0.000
43	4	82	ALA	0	-0.014	0.002	41.832	-0.001	-0.001	0.000	0.000	0.000	0.000
44	4	83	LEU	0	0.006	-0.002	40.211	0.000	0.000	0.000	0.000	0.000	0.000
45	4	84	LEU	0	-0.019	-0.004	43.918	0.001	0.001	0.000	0.000	0.000	0.000
46	4	85	ALA	0	0.017	0.010	44.291	-0.001	-0.001	0.000	0.000	0.000	0.000

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