FMO DATABASE

FMODB ID: 174MZ

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-241569.883131
FMO2-HF: Nuclear repulsion	221595.155488
FMO2-HF: Total energy	-19974.727643
FMO2-MP2: Total energy	-20032.296095

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.
-2.758	-0.174	-0.001	-1.33	-1.253	0.002

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 : 0.001 / q_NPA : -0.009

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	D	12	LYS	1	0.929	0.954	3.529	-1.109	1.475	-0.001	-1.330	-1.253	0.002
4	D	13	PRO	0	0.021	0.025	6.063	-0.027	-0.027	0.000	0.000	0.000	0.000
5	D	14	MET	0	-0.043	0.001	9.740	0.020	0.020	0.000	0.000	0.000	0.000
6	D	15	ASP	-1	-0.738	-0.872	12.741	-0.290	-0.290	0.000	0.000	0.000	0.000
7	D	16	VAL	0	0.011	-0.016	15.554	-0.014	-0.014	0.000	0.000	0.000	0.000
8	D	17	GLU	-1	-0.993	-0.991	17.142	-0.159	-0.159	0.000	0.000	0.000	0.000
9	D	18	GLU	-1	-0.906	-0.959	14.179	-0.324	-0.324	0.000	0.000	0.000	0.000
10	D	19	ALA	0	0.022	0.004	12.673	0.001	0.001	0.000	0.000	0.000	0.000
11	D	20	ARG	1	0.918	0.959	13.603	0.157	0.157	0.000	0.000	0.000	0.000
12	D	21	LEU	0	-0.017	-0.001	16.497	0.023	0.023	0.000	0.000	0.000	0.000
13	D	22	GLN	0	0.042	0.001	10.829	0.070	0.070	0.000	0.000	0.000	0.000
14	D	23	MET	0	-0.053	-0.022	12.723	0.020	0.020	0.000	0.000	0.000	0.000
15	D	24	GLU	-1	-0.930	-0.963	13.601	-0.063	-0.063	0.000	0.000	0.000	0.000
16	D	25	LEU	0	-0.094	-0.033	14.256	0.029	0.029	0.000	0.000	0.000	0.000
17	D	26	LEU	0	-0.084	-0.049	8.900	0.024	0.024	0.000	0.000	0.000	0.000
18	D	27	GLY	0	0.000	0.017	13.500	0.033	0.033	0.000	0.000	0.000	0.000
19	D	28	HIS	0	-0.022	-0.003	10.881	0.020	0.020	0.000	0.000	0.000	0.000
20	D	29	ASP	-1	-0.941	-0.979	14.599	-0.022	-0.022	0.000	0.000	0.000	0.000
21	D	30	PHE	0	-0.007	-0.028	9.563	-0.010	-0.010	0.000	0.000	0.000	0.000
22	D	31	PHE	0	-0.008	0.002	8.619	-0.040	-0.040	0.000	0.000	0.000	0.000
23	D	32	ILE	0	-0.011	-0.010	6.258	0.071	0.071	0.000	0.000	0.000	0.000
24	D	33	TYR	0	-0.041	-0.024	6.728	-0.458	-0.458	0.000	0.000	0.000	0.000
25	D	34	THR	0	-0.044	-0.042	7.250	0.076	0.076	0.000	0.000	0.000	0.000
26	D	35	ASP	-1	-0.901	-0.940	9.548	-0.312	-0.312	0.000	0.000	0.000	0.000
27	D	36	SER	0	-0.066	-0.050	11.674	0.028	0.028	0.000	0.000	0.000	0.000
28	D	37	GLU	-1	-0.937	-0.954	12.227	-0.400	-0.400	0.000	0.000	0.000	0.000
29	D	38	ASP	-1	-0.990	-0.971	14.466	-0.220	-0.220	0.000	0.000	0.000	0.000
30	D	39	GLY	0	0.030	0.022	14.492	0.030	0.030	0.000	0.000	0.000	0.000
31	D	40	ALA	0	-0.047	-0.036	13.135	-0.015	-0.015	0.000	0.000	0.000	0.000
32	D	41	THR	0	-0.010	-0.020	8.845	-0.097	-0.097	0.000	0.000	0.000	0.000
33	D	42	ASN	0	0.098	0.036	10.815	0.168	0.168	0.000	0.000	0.000	0.000
34	D	43	ILE	0	-0.015	-0.008	10.694	-0.122	-0.122	0.000	0.000	0.000	0.000
35	D	44	LEU	0	0.010	0.036	12.579	0.069	0.069	0.000	0.000	0.000	0.000
36	D	45	TYR	0	-0.002	-0.021	13.939	0.000	0.000	0.000	0.000	0.000	0.000
37	D	46	ARG	1	0.928	0.987	16.492	0.072	0.072	0.000	0.000	0.000	0.000
38	D	47	ARG	1	0.919	0.958	19.779	0.079	0.079	0.000	0.000	0.000	0.000
39	D	48	GLU	-1	-0.894	-0.959	22.558	0.006	0.006	0.000	0.000	0.000	0.000
40	D	49	ASP	-1	-0.912	-0.953	25.379	-0.043	-0.043	0.000	0.000	0.000	0.000
41	D	50	GLY	0	0.006	0.007	24.619	0.000	0.000	0.000	0.000	0.000	0.000
42	D	51	ASN	0	-0.099	-0.042	24.238	-0.010	-0.010	0.000	0.000	0.000	0.000
43	D	52	LEU	0	0.000	-0.008	19.081	0.001	0.001	0.000	0.000	0.000	0.000
44	D	53	GLY	0	-0.055	-0.013	19.746	0.005	0.005	0.000	0.000	0.000	0.000
45	D	54	LEU	0	0.006	-0.012	15.587	-0.017	-0.017	0.000	0.000	0.000	0.000
46	D	55	ILE	0	-0.044	-0.027	15.364	0.025	0.025	0.000	0.000	0.000	0.000
47	D	56	GLU	-1	-0.836	-0.900	14.926	-0.251	-0.251	0.000	0.000	0.000	0.000
48	D	57	ALA	0	-0.066	-0.044	13.538	0.047	0.047	0.000	0.000	0.000	0.000
49	D	58	LYS	1	0.893	0.947	14.647	0.171	0.171	0.000	0.000	0.000	0.000

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