FMO DATABASE

FMODB ID: YVYG2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-392222.826143
FMO2-HF: Nuclear repulsion	363464.307587
FMO2-HF: Total energy	-28758.518555
FMO2-MP2: Total energy	-28840.520948

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.
0.125	2.522	0.665	-1.224	-1.838	-0.001

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 : -0.001 / 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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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	0.035	0.027	3.618	-0.751	0.910	-0.007	-0.789	-0.864	0.001
4	A	4	THR	0	-0.047	-0.020	2.559	-0.569	0.159	0.673	-0.432	-0.970	-0.002
5	A	5	ARG	1	0.965	0.981	5.058	0.265	0.273	-0.001	-0.003	-0.004	0.000
6	A	6	LYS	1	0.965	0.986	8.757	0.865	0.865	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.032	0.006	11.277	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.027	-0.002	14.148	0.017	0.017	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.012	0.002	14.805	0.003	0.003	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.025	-0.017	16.577	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.845	-0.905	20.105	0.196	0.196	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.091	-0.037	22.336	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.801	-0.894	25.949	0.077	0.077	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.088	0.031	27.579	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.061	-0.015	28.641	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	16	MET	0	0.021	-0.004	27.611	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.784	0.892	22.329	-0.131	-0.131	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.033	-0.003	25.817	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.035	-0.016	28.143	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.006	-0.002	23.751	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.026	0.013	22.612	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.023	0.024	25.840	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.006	0.007	28.015	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.741	-0.856	22.991	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.973	-0.983	25.982	0.024	0.024	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.075	-0.065	27.713	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.041	-0.027	27.036	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.030	0.028	29.045	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.027	-0.019	26.439	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.002	0.005	29.152	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.773	0.873	25.214	0.073	0.073	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.810	0.897	21.841	0.028	0.028	0.000	0.000	0.000	0.000
33	A	33	PHE	0	-0.023	-0.024	21.012	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.014	0.018	18.774	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.125	-0.052	12.735	-0.034	-0.034	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.033	-0.030	11.932	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.780	-0.876	15.781	0.135	0.135	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.107	-0.053	14.211	0.029	0.029	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.820	-0.901	17.677	0.252	0.252	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.911	-0.960	21.027	0.120	0.120	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.032	-0.030	23.496	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.065	-0.043	18.480	0.007	0.007	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.028	0.011	18.444	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.013	-0.005	11.349	0.005	0.005	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.026	0.013	16.143	-0.027	-0.027	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.034	-0.020	16.431	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.013	0.010	16.518	0.022	0.022	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.882	-0.954	18.375	-0.158	-0.158	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.024	0.013	21.224	0.003	0.003	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.021	0.002	23.116	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.000	-0.001	25.147	0.009	0.009	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.018	0.010	24.022	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.006	0.007	26.873	0.004	0.004	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.040	-0.023	29.157	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.838	-0.915	28.498	-0.079	-0.079	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.822	0.908	31.049	0.037	0.037	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.007	-0.021	32.802	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.009	0.008	34.914	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.897	-0.942	34.057	-0.045	-0.045	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.074	-0.031	36.219	0.002	0.002	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.041	0.003	39.544	0.004	0.004	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.911	-0.949	42.011	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.042	0.044	42.026	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.017	-0.031	44.605	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.013	-0.001	48.147	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.010	0.011	46.431	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.011	-0.013	44.043	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.052	0.013	43.283	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.022	-0.007	44.340	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.076	-0.039	41.535	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.880	0.972	38.942	0.041	0.041	0.000	0.000	0.000	0.000

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