FMO DATABASE

FMODB ID: 5J4VZ

Calculation Name: 1JY2-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JY2

Chain ID: N

ChEMBL ID:

UniProt ID: P02672

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	43
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-162650.496135
FMO2-HF: Nuclear repulsion	144218.814691
FMO2-HF: Total energy	-18431.681445
FMO2-MP2: Total energy	-18482.376653

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(N:35:GLY)

Summations of interaction energy for fragment #1(N:35:GLY)

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.
-0.425	0.429	-0.004	-0.391	-0.46	0.001

Interaction energy analysis for fragmet #1(N:35:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.015

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	N	37	PRO	0	0.009	0.012	3.847	-0.333	0.521	-0.004	-0.391	-0.460	0.001
4	N	38	PHE	0	-0.011	-0.018	6.606	0.459	0.459	0.000	0.000	0.000	0.000
5	N	39	CYS	0	-0.072	-0.027	8.943	-0.070	-0.070	0.000	0.000	0.000	0.000
6	N	40	SER	0	0.011	-0.015	12.016	0.028	0.028	0.000	0.000	0.000	0.000
7	N	41	ASP	-1	-0.888	-0.966	15.440	0.038	0.038	0.000	0.000	0.000	0.000
8	N	42	GLU	-1	-0.957	-0.977	18.787	-0.069	-0.069	0.000	0.000	0.000	0.000
9	N	43	ASP	-1	-0.805	-0.863	14.424	-0.150	-0.150	0.000	0.000	0.000	0.000
10	N	44	TRP	0	0.039	0.021	16.792	0.046	0.046	0.000	0.000	0.000	0.000
11	N	45	ASN	0	-0.052	-0.033	18.725	-0.012	-0.012	0.000	0.000	0.000	0.000
12	N	46	THR	0	-0.030	-0.005	18.169	0.001	0.001	0.000	0.000	0.000	0.000
13	N	47	LYS	1	0.819	0.900	12.047	0.162	0.162	0.000	0.000	0.000	0.000
14	N	48	CYS	0	-0.011	-0.003	15.859	-0.004	-0.004	0.000	0.000	0.000	0.000
15	N	49	PRO	0	0.020	0.008	14.623	0.051	0.051	0.000	0.000	0.000	0.000
16	N	50	SER	0	0.015	0.013	14.168	-0.066	-0.066	0.000	0.000	0.000	0.000
17	N	51	GLY	0	0.084	0.027	15.962	-0.003	-0.003	0.000	0.000	0.000	0.000
18	N	52	CYS	0	-0.008	-0.004	17.441	-0.016	-0.016	0.000	0.000	0.000	0.000
19	N	53	ARG	1	0.940	0.980	13.861	-0.561	-0.561	0.000	0.000	0.000	0.000
20	N	54	MET	0	0.036	0.015	18.140	-0.007	-0.007	0.000	0.000	0.000	0.000
21	N	55	LYS	1	0.822	0.888	20.964	-0.176	-0.176	0.000	0.000	0.000	0.000
22	N	56	GLY	0	0.027	0.017	21.665	-0.014	-0.014	0.000	0.000	0.000	0.000
23	N	57	LEU	0	0.011	-0.004	19.187	-0.006	-0.006	0.000	0.000	0.000	0.000
24	N	58	ILE	0	-0.018	-0.004	23.120	-0.018	-0.018	0.000	0.000	0.000	0.000
25	N	59	ASP	-1	-0.795	-0.874	25.959	0.150	0.150	0.000	0.000	0.000	0.000
26	N	60	GLU	-1	-0.970	-0.982	23.402	0.221	0.221	0.000	0.000	0.000	0.000
27	N	61	VAL	0	-0.005	-0.007	26.548	-0.012	-0.012	0.000	0.000	0.000	0.000
28	N	62	ASP	-1	-0.892	-0.929	28.881	0.094	0.094	0.000	0.000	0.000	0.000
29	N	63	GLN	0	0.000	-0.002	30.281	-0.008	-0.008	0.000	0.000	0.000	0.000
30	N	64	ASP	-1	-0.793	-0.892	30.509	0.107	0.107	0.000	0.000	0.000	0.000
31	N	65	PHE	0	-0.023	-0.017	31.906	-0.010	-0.010	0.000	0.000	0.000	0.000
32	N	66	THR	0	-0.004	-0.009	34.790	-0.010	-0.010	0.000	0.000	0.000	0.000
33	N	67	SER	0	-0.050	-0.013	34.986	-0.009	-0.009	0.000	0.000	0.000	0.000
34	N	68	ARG	1	0.812	0.885	32.883	-0.105	-0.105	0.000	0.000	0.000	0.000
35	N	69	ILE	0	0.016	0.002	38.238	-0.006	-0.006	0.000	0.000	0.000	0.000
36	N	70	ASN	0	-0.011	-0.007	40.013	-0.008	-0.008	0.000	0.000	0.000	0.000
37	N	71	LYS	1	0.960	0.985	37.090	-0.093	-0.093	0.000	0.000	0.000	0.000
38	N	72	LEU	0	-0.011	0.004	41.485	-0.003	-0.003	0.000	0.000	0.000	0.000
39	N	73	ARG	1	0.920	0.967	42.461	-0.066	-0.066	0.000	0.000	0.000	0.000
40	N	74	ASP	-1	-0.872	-0.930	44.407	0.060	0.060	0.000	0.000	0.000	0.000
41	N	75	SER	0	-0.130	-0.069	46.271	-0.003	-0.003	0.000	0.000	0.000	0.000
42	N	76	LEU	0	-0.036	-0.009	48.201	-0.002	-0.002	0.000	0.000	0.000	0.000
43	N	77	PHE	0	-0.075	-0.041	49.025	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(N:35:GLY)