FMO DATABASE

FMODB ID: YZ9R2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-140310.392284
FMO2-HF: Nuclear repulsion	122327.708373
FMO2-HF: Total energy	-17982.683911
FMO2-MP2: Total energy	-18033.837653

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.
-3.121	-0.305	0.241	-1.492	-1.565	0.004

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 : 0.016

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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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	-0.016	-0.011	3.869	-2.537	-0.691	-0.013	-1.037	-0.796	0.004
4	4	18	THR	0	-0.051	-0.040	2.612	-0.861	0.029	0.255	-0.442	-0.703	0.000
5	4	19	GLY	0	0.059	0.029	4.412	-0.517	-0.437	-0.001	-0.013	-0.066	0.000
6	4	20	SER	0	-0.030	-0.008	6.904	0.147	0.147	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.004	0.010	8.072	0.149	0.149	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.040	-0.015	10.342	0.041	0.041	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.031	0.006	10.180	0.111	0.111	0.000	0.000	0.000	0.000
10	4	24	ASN	0	-0.044	-0.033	9.563	-0.133	-0.133	0.000	0.000	0.000	0.000
11	4	25	TYR	0	-0.012	0.001	11.501	0.009	0.009	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.002	0.010	13.514	-0.003	-0.003	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.041	0.010	12.624	0.042	0.042	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.073	0.028	8.294	-0.083	-0.083	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.008	-0.016	11.037	0.029	0.029	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.034	-0.017	13.694	-0.023	-0.023	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.036	0.006	8.900	-0.071	-0.071	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.021	-0.023	6.508	-0.040	-0.040	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.039	0.030	10.072	-0.079	-0.079	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.037	-0.015	10.537	0.131	0.131	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.898	-0.936	9.656	0.912	0.912	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.051	-0.035	12.931	-0.069	-0.069	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.001	0.003	14.227	0.052	0.052	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.035	0.019	17.881	-0.019	-0.019	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.047	-0.019	21.232	-0.011	-0.011	0.000	0.000	0.000	0.000
26	4	65	ASP	-1	-0.879	-0.950	10.433	-0.316	-0.316	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.802	-0.915	12.171	0.091	0.091	0.000	0.000	0.000	0.000
28	4	67	TRP	0	-0.002	0.014	14.539	-0.020	-0.020	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.055	0.014	16.104	-0.008	-0.008	0.000	0.000	0.000	0.000
30	4	69	SER	0	-0.003	0.022	14.329	-0.014	-0.014	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.823	0.899	16.456	-0.033	-0.033	0.000	0.000	0.000	0.000
32	4	71	LEU	0	-0.001	0.008	19.436	-0.001	-0.001	0.000	0.000	0.000	0.000
33	4	72	ALA	0	-0.001	0.009	19.089	0.001	0.001	0.000	0.000	0.000	0.000
34	4	73	SER	0	-0.039	-0.038	19.033	-0.007	-0.007	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.101	-0.053	21.670	0.009	0.009	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.004	0.010	24.615	0.008	0.008	0.000	0.000	0.000	0.000
37	4	76	PHE	0	-0.023	-0.006	26.525	-0.003	-0.003	0.000	0.000	0.000	0.000
38	4	77	SER	0	-0.019	-0.018	27.869	-0.005	-0.005	0.000	0.000	0.000	0.000
39	4	78	GLY	0	0.006	0.001	30.432	-0.002	-0.002	0.000	0.000	0.000	0.000
40	4	79	LEU	0	-0.007	0.000	34.150	0.000	0.000	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.012	-0.010	37.497	0.002	0.002	0.000	0.000	0.000	0.000
42	4	81	GLY	0	0.010	0.002	39.232	0.003	0.003	0.000	0.000	0.000	0.000
43	4	82	ALA	0	-0.024	-0.005	42.088	-0.002	-0.002	0.000	0.000	0.000	0.000
44	4	83	LEU	0	0.019	0.011	40.908	-0.001	-0.001	0.000	0.000	0.000	0.000
45	4	84	LEU	0	-0.019	-0.007	44.612	0.002	0.002	0.000	0.000	0.000	0.000
46	4	85	ALA	0	0.013	0.012	44.325	-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)