FMO DATABASE

FMODB ID: JQ139

Calculation Name: 1YTF-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YTF

Chain ID: D

ChEMBL ID:

UniProt ID: P32774

Base Structure: X-ray

Registration Date: 2023-09-24

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-636916.419287
FMO2-HF: Nuclear repulsion	597323.380939
FMO2-HF: Total energy	-39593.038348
FMO2-MP2: Total energy	-39707.150585

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:5:GLY)

Summations of interaction energy for fragment #1(D:5: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.
-2.658	-1.264	-0.001	-0.93	-0.464	0.004

Interaction energy analysis for fragmet #1(D:5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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	D	7	TYR	0	-0.003	-0.022	3.870	-1.716	-0.322	-0.001	-0.930	-0.464	0.004
4	D	8	GLU	-1	-0.783	-0.886	6.793	-1.356	-1.356	0.000	0.000	0.000	0.000
5	D	9	LEU	0	-0.061	-0.025	9.120	0.377	0.377	0.000	0.000	0.000	0.000
6	D	10	TYR	0	0.047	0.013	9.724	0.226	0.226	0.000	0.000	0.000	0.000
7	D	11	ARG	1	0.802	0.882	8.504	2.080	2.080	0.000	0.000	0.000	0.000
8	D	12	ARG	1	0.948	0.984	14.560	0.729	0.729	0.000	0.000	0.000	0.000
9	D	13	SER	0	-0.034	-0.015	16.588	0.108	0.108	0.000	0.000	0.000	0.000
10	D	14	THR	0	0.022	-0.004	18.737	-0.012	-0.012	0.000	0.000	0.000	0.000
11	D	15	ILE	0	0.029	0.026	17.741	0.018	0.018	0.000	0.000	0.000	0.000
12	D	16	GLY	0	0.006	0.011	16.843	-0.011	-0.011	0.000	0.000	0.000	0.000
13	D	17	ASN	0	-0.018	-0.023	17.535	-0.029	-0.029	0.000	0.000	0.000	0.000
14	D	18	SER	0	0.037	0.006	20.257	0.027	0.027	0.000	0.000	0.000	0.000
15	D	19	LEU	0	-0.052	-0.010	15.605	0.027	0.027	0.000	0.000	0.000	0.000
16	D	20	VAL	0	0.006	-0.003	16.800	0.002	0.002	0.000	0.000	0.000	0.000
17	D	21	ASP	-1	-0.870	-0.930	19.269	-0.339	-0.339	0.000	0.000	0.000	0.000
18	D	22	ALA	0	-0.030	-0.003	22.060	0.035	0.035	0.000	0.000	0.000	0.000
19	D	23	LEU	0	-0.037	-0.025	16.837	0.025	0.025	0.000	0.000	0.000	0.000
20	D	24	ASP	-1	-0.869	-0.938	20.375	-0.409	-0.409	0.000	0.000	0.000	0.000
21	D	25	THR	0	-0.035	-0.020	22.664	0.042	0.042	0.000	0.000	0.000	0.000
22	D	26	LEU	0	-0.013	-0.013	22.909	0.024	0.024	0.000	0.000	0.000	0.000
23	D	27	ILE	0	-0.036	-0.016	19.936	0.020	0.020	0.000	0.000	0.000	0.000
24	D	28	SER	0	-0.078	-0.054	24.581	0.025	0.025	0.000	0.000	0.000	0.000
25	D	29	ASP	-1	-0.996	-0.986	27.464	-0.165	-0.165	0.000	0.000	0.000	0.000
26	D	30	GLY	0	0.015	0.019	28.477	0.014	0.014	0.000	0.000	0.000	0.000
27	D	31	ARG	1	0.855	0.919	27.747	0.170	0.170	0.000	0.000	0.000	0.000
28	D	32	ILE	0	-0.048	-0.015	22.392	0.006	0.006	0.000	0.000	0.000	0.000
29	D	33	GLU	-1	-0.889	-0.954	20.904	-0.218	-0.218	0.000	0.000	0.000	0.000
30	D	34	ALA	0	0.083	0.038	19.619	-0.043	-0.043	0.000	0.000	0.000	0.000
31	D	35	SER	0	-0.021	-0.016	15.696	0.015	0.015	0.000	0.000	0.000	0.000
32	D	36	LEU	0	-0.024	-0.008	14.906	-0.070	-0.070	0.000	0.000	0.000	0.000
33	D	37	ALA	0	0.064	0.024	15.785	-0.059	-0.059	0.000	0.000	0.000	0.000
34	D	38	MET	0	-0.016	0.001	9.960	-0.051	-0.051	0.000	0.000	0.000	0.000
35	D	39	ARG	1	0.866	0.901	9.501	0.406	0.406	0.000	0.000	0.000	0.000
36	D	40	VAL	0	-0.004	0.017	11.956	-0.098	-0.098	0.000	0.000	0.000	0.000
37	D	41	LEU	0	0.022	0.010	11.562	-0.066	-0.066	0.000	0.000	0.000	0.000
38	D	42	GLU	-1	-0.810	-0.887	7.272	-1.212	-1.212	0.000	0.000	0.000	0.000
39	D	43	THR	0	-0.061	-0.034	8.151	-0.247	-0.247	0.000	0.000	0.000	0.000
40	D	44	PHE	0	-0.006	0.000	10.859	0.023	0.023	0.000	0.000	0.000	0.000
41	D	45	ASP	-1	-0.793	-0.884	7.650	-2.281	-2.281	0.000	0.000	0.000	0.000
42	D	46	LYS	1	0.804	0.886	6.741	0.697	0.697	0.000	0.000	0.000	0.000
43	D	47	VAL	0	0.038	0.020	8.094	0.282	0.282	0.000	0.000	0.000	0.000
44	D	48	VAL	0	-0.009	0.016	11.850	0.174	0.174	0.000	0.000	0.000	0.000
45	D	49	ALA	0	0.002	-0.001	8.597	0.147	0.147	0.000	0.000	0.000	0.000
46	D	50	GLU	-1	-0.798	-0.877	8.921	-0.445	-0.445	0.000	0.000	0.000	0.000
47	D	51	THR	0	0.003	-0.011	11.819	0.137	0.137	0.000	0.000	0.000	0.000
48	D	52	LEU	0	-0.053	-0.037	13.615	0.089	0.089	0.000	0.000	0.000	0.000
49	D	53	LYS	1	0.754	0.881	10.880	0.290	0.290	0.000	0.000	0.000	0.000
50	D	54	ASP	-1	-0.803	-0.872	14.273	-0.156	-0.156	0.000	0.000	0.000	0.000
51	D	55	ASN	0	-0.068	-0.043	16.988	0.010	0.010	0.000	0.000	0.000	0.000
52	D	56	THR	0	-0.047	-0.018	18.210	0.018	0.018	0.000	0.000	0.000	0.000
53	D	57	GLN	0	-0.029	-0.030	20.766	0.027	0.027	0.000	0.000	0.000	0.000
54	D	58	SER	0	-0.039	-0.034	23.680	0.006	0.006	0.000	0.000	0.000	0.000
55	D	59	LYS	1	0.877	0.946	23.541	0.097	0.097	0.000	0.000	0.000	0.000
56	D	60	LEU	0	0.024	0.008	22.630	0.008	0.008	0.000	0.000	0.000	0.000
57	D	61	THR	0	-0.040	-0.027	25.707	0.013	0.013	0.000	0.000	0.000	0.000
58	D	62	VAL	0	0.014	0.011	25.806	-0.002	-0.002	0.000	0.000	0.000	0.000
59	D	63	LYS	1	0.957	0.981	28.526	0.095	0.095	0.000	0.000	0.000	0.000
60	D	64	GLY	0	0.050	0.017	31.376	-0.005	-0.005	0.000	0.000	0.000	0.000
61	D	65	ASN	0	-0.012	0.013	32.373	0.008	0.008	0.000	0.000	0.000	0.000
62	D	66	LEU	0	0.012	0.000	26.816	-0.012	-0.012	0.000	0.000	0.000	0.000
63	D	67	ASP	-1	-0.760	-0.856	29.796	-0.133	-0.133	0.000	0.000	0.000	0.000
64	D	68	THR	0	-0.044	-0.037	26.106	0.001	0.001	0.000	0.000	0.000	0.000
65	D	69	TYR	0	-0.014	-0.010	24.631	-0.012	-0.012	0.000	0.000	0.000	0.000
66	D	70	GLY	0	0.021	0.014	22.898	0.011	0.011	0.000	0.000	0.000	0.000
67	D	71	PHE	0	-0.035	-0.016	15.752	-0.023	-0.023	0.000	0.000	0.000	0.000
68	D	72	CYS	0	-0.026	-0.022	17.516	0.045	0.045	0.000	0.000	0.000	0.000
69	D	73	ASP	-1	-0.847	-0.911	13.029	-0.195	-0.195	0.000	0.000	0.000	0.000
70	D	74	ASP	-1	-0.824	-0.901	11.337	-0.034	-0.034	0.000	0.000	0.000	0.000
71	D	75	VAL	0	-0.040	-0.022	12.124	-0.095	-0.095	0.000	0.000	0.000	0.000
72	D	76	TRP	0	0.015	0.015	14.490	0.052	0.052	0.000	0.000	0.000	0.000
73	D	77	THR	0	-0.045	-0.037	17.487	-0.072	-0.072	0.000	0.000	0.000	0.000
74	D	78	PHE	0	0.005	-0.005	20.022	0.036	0.036	0.000	0.000	0.000	0.000
75	D	79	ILE	0	-0.040	-0.026	23.500	-0.027	-0.027	0.000	0.000	0.000	0.000
76	D	80	VAL	0	0.005	0.019	26.464	0.018	0.018	0.000	0.000	0.000	0.000
77	D	81	LYS	1	0.855	0.897	28.982	0.120	0.120	0.000	0.000	0.000	0.000
78	D	82	ASN	0	-0.027	-0.022	32.572	0.006	0.006	0.000	0.000	0.000	0.000
79	D	83	CYS	0	-0.058	-0.011	30.480	0.002	0.002	0.000	0.000	0.000	0.000
80	D	84	GLN	0	0.004	-0.009	32.555	0.003	0.003	0.000	0.000	0.000	0.000
81	D	85	VAL	0	0.002	-0.015	27.814	-0.003	-0.003	0.000	0.000	0.000	0.000
82	D	86	THR	0	-0.008	0.001	30.464	0.004	0.004	0.000	0.000	0.000	0.000
83	D	87	VAL	0	0.007	-0.002	27.889	-0.011	-0.011	0.000	0.000	0.000	0.000
84	D	88	GLU	-1	-0.829	-0.881	27.997	-0.127	-0.127	0.000	0.000	0.000	0.000
85	D	104	SER	0	0.045	0.030	33.040	0.003	0.003	0.000	0.000	0.000	0.000
86	D	105	VAL	0	-0.042	-0.043	33.363	-0.002	-0.002	0.000	0.000	0.000	0.000
87	D	106	ILE	0	0.026	0.033	30.957	0.002	0.002	0.000	0.000	0.000	0.000
88	D	107	SER	0	-0.032	-0.037	33.627	0.008	0.008	0.000	0.000	0.000	0.000
89	D	108	VAL	0	0.017	0.013	29.752	-0.004	-0.004	0.000	0.000	0.000	0.000
90	D	109	ASP	-1	-0.857	-0.908	32.792	-0.131	-0.131	0.000	0.000	0.000	0.000
91	D	110	LYS	1	0.852	0.907	28.950	0.178	0.178	0.000	0.000	0.000	0.000
92	D	111	LEU	0	0.029	0.026	24.998	-0.009	-0.009	0.000	0.000	0.000	0.000
93	D	112	ARG	1	0.936	0.978	21.522	0.292	0.292	0.000	0.000	0.000	0.000
94	D	113	ILE	0	0.010	0.002	19.819	-0.016	-0.016	0.000	0.000	0.000	0.000
95	D	114	VAL	0	-0.017	-0.020	15.454	0.021	0.021	0.000	0.000	0.000	0.000
96	D	115	ALA	0	-0.011	-0.003	14.610	-0.040	-0.040	0.000	0.000	0.000	0.000
97	D	116	CYS	0	0.025	0.030	9.669	0.003	0.003	0.000	0.000	0.000	0.000
98	D	117	ASN	0	0.004	0.004	10.625	0.020	0.020	0.000	0.000	0.000	0.000
99	D	118	SER	0	0.002	0.017	9.497	-0.042	-0.042	0.000	0.000	0.000	0.000
100	D	119	LYS	1	0.887	0.939	7.731	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:5:GLY)