FMO DATABASE

FMODB ID: 5J36Z

Calculation Name: 1YDL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YDL

Chain ID: A

ChEMBL ID:

UniProt ID: Q6ZYL4

Base Structure: X-ray

Registration Date: 2023-09-21

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-391860.691646
FMO2-HF: Nuclear repulsion	363102.350367
FMO2-HF: Total energy	-28758.34128
FMO2-MP2: Total energy	-28840.345635

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(A:1:SER)

Summations of interaction energy for fragment #1(A:1: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.
0.55	3.126	0.268	-1.214	-1.63	0.003

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / 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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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	A	3	GLY	0	0.031	0.025	3.799	-0.438	1.456	-0.020	-0.979	-0.895	0.004
4	A	4	THR	0	-0.034	-0.025	2.951	0.165	0.847	0.289	-0.235	-0.736	-0.001
5	A	5	ARG	1	0.976	0.989	5.380	-0.190	-0.190	-0.001	0.000	0.001	0.000
6	A	6	LYS	1	0.964	0.982	9.022	0.054	0.054	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.033	0.005	11.471	-0.124	-0.124	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.025	-0.004	14.367	0.075	0.075	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.016	0.009	14.764	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.032	-0.019	16.844	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.841	-0.911	20.375	0.429	0.429	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.099	-0.047	22.491	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.821	-0.900	26.008	0.177	0.177	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.092	0.026	27.906	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.063	-0.017	28.958	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	MET	0	0.026	-0.007	27.756	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.821	0.897	22.297	-0.210	-0.210	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.017	-0.003	26.129	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.014	-0.004	28.433	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.000	0.011	23.745	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.031	0.011	22.620	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.012	0.020	25.951	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.014	-0.001	28.014	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.755	-0.875	23.044	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.972	-0.986	26.026	0.015	0.015	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.069	-0.053	27.665	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.037	-0.022	27.408	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.045	0.041	29.524	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.012	-0.016	26.880	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.019	-0.001	29.718	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.803	0.868	25.014	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.812	0.915	22.072	0.025	0.025	0.000	0.000	0.000	0.000
33	A	33	PHE	0	-0.022	-0.026	21.167	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.009	0.010	19.054	0.034	0.034	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.111	-0.039	12.970	-0.050	-0.050	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.041	-0.035	11.807	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.795	-0.874	15.793	0.235	0.235	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.093	-0.058	14.032	0.036	0.036	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.821	-0.888	17.610	0.339	0.339	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.931	-0.974	20.677	0.212	0.212	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.037	-0.024	23.093	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.042	-0.033	18.395	0.023	0.023	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.024	0.009	18.462	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.021	0.002	11.434	0.045	0.045	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.012	-0.003	16.070	-0.071	-0.071	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.040	-0.023	16.671	0.040	0.040	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.014	0.001	16.643	0.025	0.025	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.913	-0.959	18.414	0.062	0.062	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.040	0.018	21.641	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.026	0.007	23.355	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.032	0.011	25.467	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.032	0.024	24.353	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.010	0.008	27.173	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.066	-0.042	29.453	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.878	-0.916	29.334	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.826	0.907	31.244	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.007	-0.017	32.961	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.013	0.015	35.198	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.907	-0.943	34.892	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.079	-0.033	36.520	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.058	-0.011	39.753	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.917	-0.947	42.209	0.018	0.018	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.026	0.023	43.701	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.020	-0.024	45.419	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.012	-0.008	48.620	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.020	0.009	46.916	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.027	-0.040	44.420	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.036	0.022	43.440	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.033	-0.015	44.358	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.046	-0.019	41.908	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.936	1.003	39.359	0.001	0.001	0.000	0.000	0.000	0.000

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