FMO DATABASE

FMODB ID: G6NJ1

Calculation Name: 3LYV-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYV

Chain ID: D

ChEMBL ID:

UniProt ID: Q5XAQ7

Base Structure: X-ray

Registration Date: 2023-06-21

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-241942.468018
FMO2-HF: Nuclear repulsion	221967.259138
FMO2-HF: Total energy	-19975.20888
FMO2-MP2: Total energy	-20032.755693

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:10:THR)

Summations of interaction energy for fragment #1(D:10:THR)

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.
-4.085	-1.352	-0.002	-1.445	-1.287	0.003

Interaction energy analysis for fragmet #1(D:10:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.010

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	D	12	LYS	1	0.945	0.964	3.505	-1.170	1.563	-0.002	-1.445	-1.287	0.003
4	D	13	PRO	0	0.026	0.029	6.033	-0.261	-0.261	0.000	0.000	0.000	0.000
5	D	14	MET	0	-0.053	-0.007	9.713	0.032	0.032	0.000	0.000	0.000	0.000
6	D	15	ASP	-1	-0.759	-0.879	12.686	-0.366	-0.366	0.000	0.000	0.000	0.000
7	D	16	VAL	0	0.004	-0.008	15.522	-0.053	-0.053	0.000	0.000	0.000	0.000
8	D	17	GLU	-1	-0.874	-0.910	17.366	-0.275	-0.275	0.000	0.000	0.000	0.000
9	D	18	GLU	-1	-0.882	-0.962	13.978	-0.226	-0.226	0.000	0.000	0.000	0.000
10	D	19	ALA	0	0.015	0.009	12.769	-0.034	-0.034	0.000	0.000	0.000	0.000
11	D	20	ARG	1	0.831	0.897	13.740	0.241	0.241	0.000	0.000	0.000	0.000
12	D	21	LEU	0	-0.018	-0.008	16.505	0.005	0.005	0.000	0.000	0.000	0.000
13	D	22	GLN	0	-0.018	-0.024	10.775	0.103	0.103	0.000	0.000	0.000	0.000
14	D	23	MET	0	-0.048	-0.022	12.920	-0.049	-0.049	0.000	0.000	0.000	0.000
15	D	24	GLU	-1	-0.865	-0.913	13.778	-0.356	-0.356	0.000	0.000	0.000	0.000
16	D	25	LEU	0	-0.087	-0.032	14.162	0.044	0.044	0.000	0.000	0.000	0.000
17	D	26	LEU	0	-0.069	-0.041	8.715	0.009	0.009	0.000	0.000	0.000	0.000
18	D	27	GLY	0	-0.004	0.014	13.447	0.011	0.011	0.000	0.000	0.000	0.000
19	D	28	HIS	0	-0.008	0.006	10.836	0.069	0.069	0.000	0.000	0.000	0.000
20	D	29	ASP	-1	-0.935	-0.975	14.956	-0.558	-0.558	0.000	0.000	0.000	0.000
21	D	30	PHE	0	-0.006	-0.019	9.757	-0.011	-0.011	0.000	0.000	0.000	0.000
22	D	31	PHE	0	-0.014	-0.003	8.353	-0.170	-0.170	0.000	0.000	0.000	0.000
23	D	32	ILE	0	-0.015	-0.012	6.498	0.158	0.158	0.000	0.000	0.000	0.000
24	D	33	TYR	0	-0.030	-0.016	7.101	-0.680	-0.680	0.000	0.000	0.000	0.000
25	D	34	THR	0	-0.021	-0.031	7.270	-0.089	-0.089	0.000	0.000	0.000	0.000
26	D	35	ASP	-1	-0.860	-0.935	9.529	-0.358	-0.358	0.000	0.000	0.000	0.000
27	D	36	SER	0	-0.075	-0.050	11.836	0.092	0.092	0.000	0.000	0.000	0.000
28	D	37	GLU	-1	-0.942	-0.951	11.988	-0.203	-0.203	0.000	0.000	0.000	0.000
29	D	38	ASP	-1	-0.990	-0.972	14.325	-0.218	-0.218	0.000	0.000	0.000	0.000
30	D	39	GLY	0	0.039	0.018	14.470	0.018	0.018	0.000	0.000	0.000	0.000
31	D	40	ALA	0	-0.067	-0.043	13.148	-0.017	-0.017	0.000	0.000	0.000	0.000
32	D	41	THR	0	-0.004	-0.014	8.841	-0.094	-0.094	0.000	0.000	0.000	0.000
33	D	42	ASN	0	0.037	0.005	10.811	0.220	0.220	0.000	0.000	0.000	0.000
34	D	43	ILE	0	-0.011	-0.004	10.768	-0.281	-0.281	0.000	0.000	0.000	0.000
35	D	44	LEU	0	0.026	0.047	12.733	0.166	0.166	0.000	0.000	0.000	0.000
36	D	45	TYR	0	0.002	-0.015	14.206	-0.074	-0.074	0.000	0.000	0.000	0.000
37	D	46	ARG	1	0.843	0.913	16.749	0.494	0.494	0.000	0.000	0.000	0.000
38	D	47	ARG	1	0.855	0.922	20.042	0.281	0.281	0.000	0.000	0.000	0.000
39	D	48	GLU	-1	-0.885	-0.950	22.747	-0.233	-0.233	0.000	0.000	0.000	0.000
40	D	49	ASP	-1	-0.877	-0.921	25.533	-0.243	-0.243	0.000	0.000	0.000	0.000
41	D	50	GLY	0	0.019	0.012	24.905	0.016	0.016	0.000	0.000	0.000	0.000
42	D	51	ASN	0	-0.118	-0.062	24.576	-0.002	-0.002	0.000	0.000	0.000	0.000
43	D	52	LEU	0	0.017	0.003	19.503	-0.020	-0.020	0.000	0.000	0.000	0.000
44	D	53	GLY	0	-0.054	-0.013	20.018	0.034	0.034	0.000	0.000	0.000	0.000
45	D	54	LEU	0	-0.001	-0.016	15.887	-0.043	-0.043	0.000	0.000	0.000	0.000
46	D	55	ILE	0	-0.049	-0.027	15.269	0.058	0.058	0.000	0.000	0.000	0.000
47	D	56	GLU	-1	-0.796	-0.852	14.976	-0.513	-0.513	0.000	0.000	0.000	0.000
48	D	57	ALA	0	-0.056	-0.037	13.517	0.067	0.067	0.000	0.000	0.000	0.000
49	D	58	LYS	1	0.846	0.898	14.654	0.394	0.394	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:10:THR)