FMO DATABASE

FMODB ID: 142MZ

Calculation Name: 1YTF-D-Xray319

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-647571.288208
FMO2-HF: Nuclear repulsion	607637.217919
FMO2-HF: Total energy	-39934.07029
FMO2-MP2: Total energy	-40049.276646

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:4:ACE )

Summations of interaction energy for fragment #1(D:4:ACE )

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.
1.587	2.199	-0.006	-0.298	-0.308	0

Interaction energy analysis for fragmet #1(D:4:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.005

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].
3	D	6	TYR	0	-0.009	-0.007	3.838	1.095	1.707	-0.006	-0.298	-0.308
4	D	7	TYR	0	0.011	0.005	6.497	0.065	0.065	0.000	0.000	0.000
5	D	8	GLU	-1	-0.869	-0.934	8.331	0.162	0.162	0.000	0.000	0.000
6	D	9	LEU	0	-0.047	-0.034	10.685	0.070	0.070	0.000	0.000	0.000
7	D	10	TYR	0	0.037	0.005	13.589	0.035	0.035	0.000	0.000	0.000
8	D	11	ARG	1	0.885	0.937	9.967	0.013	0.013	0.000	0.000	0.000
9	D	12	ARG	1	0.936	0.974	16.212	0.113	0.113	0.000	0.000	0.000
10	D	13	SER	0	-0.038	-0.021	18.800	0.009	0.009	0.000	0.000	0.000
11	D	14	THR	0	0.036	0.010	20.778	0.008	0.008	0.000	0.000	0.000
12	D	15	ILE	0	0.022	0.012	20.018	0.009	0.009	0.000	0.000	0.000
13	D	16	GLY	0	0.009	0.006	18.578	0.006	0.006	0.000	0.000	0.000
14	D	17	ASN	0	0.000	-0.010	19.237	0.021	0.021	0.000	0.000	0.000
15	D	18	SER	0	0.005	0.004	21.517	0.012	0.012	0.000	0.000	0.000
16	D	19	LEU	0	-0.041	-0.004	17.103	0.008	0.008	0.000	0.000	0.000
17	D	20	VAL	0	-0.013	-0.012	17.830	0.012	0.012	0.000	0.000	0.000
18	D	21	ASP	-1	-0.843	-0.919	20.278	0.009	0.009	0.000	0.000	0.000
19	D	22	ALA	0	-0.050	-0.019	23.329	0.006	0.006	0.000	0.000	0.000
20	D	23	LEU	0	-0.040	-0.040	18.004	0.009	0.009	0.000	0.000	0.000
21	D	24	ASP	-1	-0.876	-0.937	21.380	0.058	0.058	0.000	0.000	0.000
22	D	25	THR	0	-0.051	-0.027	23.467	0.004	0.004	0.000	0.000	0.000
23	D	26	LEU	0	-0.004	-0.015	23.748	0.003	0.003	0.000	0.000	0.000
24	D	27	ILE	0	-0.052	-0.022	20.495	0.007	0.007	0.000	0.000	0.000
25	D	28	SER	0	-0.069	-0.038	25.038	0.003	0.003	0.000	0.000	0.000
26	D	29	ASP	-1	-0.980	-0.979	27.900	0.026	0.026	0.000	0.000	0.000
27	D	30	GLY	0	-0.028	0.006	28.983	-0.002	-0.002	0.000	0.000	0.000
28	D	31	ARG	1	0.933	0.954	28.271	-0.043	-0.043	0.000	0.000	0.000
29	D	32	ILE	0	-0.054	-0.023	23.172	0.004	0.004	0.000	0.000	0.000
30	D	33	GLU	-1	-0.904	-0.961	21.160	0.090	0.090	0.000	0.000	0.000
31	D	34	ALA	0	0.102	0.066	20.129	0.002	0.002	0.000	0.000	0.000
32	D	35	SER	0	-0.019	-0.001	16.111	0.015	0.015	0.000	0.000	0.000
33	D	36	LEU	0	-0.045	-0.035	15.125	0.027	0.027	0.000	0.000	0.000
34	D	37	ALA	0	0.052	0.019	16.080	-0.007	-0.007	0.000	0.000	0.000
35	D	38	MET	0	0.007	0.006	9.947	-0.042	-0.042	0.000	0.000	0.000
36	D	39	ARG	1	0.994	0.995	11.415	-0.280	-0.280	0.000	0.000	0.000
37	D	40	VAL	0	-0.010	0.000	12.468	-0.037	-0.037	0.000	0.000	0.000
38	D	41	LEU	0	0.009	-0.003	13.102	-0.043	-0.043	0.000	0.000	0.000
39	D	42	GLU	-1	-0.890	-0.938	8.016	0.503	0.503	0.000	0.000	0.000
40	D	43	THR	0	-0.095	-0.049	9.761	-0.120	-0.120	0.000	0.000	0.000
41	D	44	PHE	0	-0.037	-0.018	12.160	-0.062	-0.062	0.000	0.000	0.000
42	D	45	ASP	-1	-0.738	-0.860	9.397	-0.189	-0.189	0.000	0.000	0.000
43	D	46	LYS	1	0.922	0.973	9.396	0.172	0.172	0.000	0.000	0.000
44	D	47	VAL	0	0.027	0.011	10.933	-0.002	-0.002	0.000	0.000	0.000
45	D	48	VAL	0	-0.019	-0.002	14.675	0.004	0.004	0.000	0.000	0.000
46	D	49	ALA	0	-0.006	-0.001	12.232	0.006	0.006	0.000	0.000	0.000
47	D	50	GLU	-1	-0.932	-0.984	13.277	-0.335	-0.335	0.000	0.000	0.000
48	D	51	THR	0	0.019	0.018	15.721	0.039	0.039	0.000	0.000	0.000
49	D	52	LEU	0	-0.064	-0.034	17.231	0.025	0.025	0.000	0.000	0.000
50	D	53	LYS	1	0.797	0.922	15.009	0.344	0.344	0.000	0.000	0.000
51	D	54	ASP	-1	-0.864	-0.930	18.539	-0.242	-0.242	0.000	0.000	0.000
52	D	55	ASN	0	-0.078	-0.045	21.192	0.009	0.009	0.000	0.000	0.000
53	D	56	THR	0	-0.042	-0.025	22.178	0.016	0.016	0.000	0.000	0.000
54	D	57	GLN	0	-0.004	-0.009	24.900	0.003	0.003	0.000	0.000	0.000
55	D	58	SER	0	-0.003	-0.004	27.891	0.002	0.002	0.000	0.000	0.000
56	D	59	LYS	1	0.988	1.024	27.455	0.095	0.095	0.000	0.000	0.000
57	D	60	LEU	0	0.006	-0.005	27.175	0.008	0.008	0.000	0.000	0.000
58	D	61	THR	0	-0.053	-0.022	29.690	-0.005	-0.005	0.000	0.000	0.000
59	D	62	VAL	0	0.021	0.013	28.659	0.005	0.005	0.000	0.000	0.000
60	D	63	LYS	1	0.954	0.976	31.681	0.064	0.064	0.000	0.000	0.000
61	D	64	GLY	0	0.052	0.018	34.535	0.003	0.003	0.000	0.000	0.000
62	D	65	ASN	0	0.001	0.021	35.339	-0.002	-0.002	0.000	0.000	0.000
63	D	66	LEU	0	-0.006	-0.007	28.805	-0.003	-0.003	0.000	0.000	0.000
64	D	67	ASP	-1	-0.911	-0.957	32.075	-0.039	-0.039	0.000	0.000	0.000
65	D	68	THR	0	-0.017	-0.017	27.489	0.005	0.005	0.000	0.000	0.000
66	D	69	TYR	0	-0.024	-0.013	26.450	-0.006	-0.006	0.000	0.000	0.000
67	D	70	GLY	0	0.020	0.006	24.156	0.009	0.009	0.000	0.000	0.000
68	D	71	PHE	0	-0.017	-0.009	17.541	-0.010	-0.010	0.000	0.000	0.000
69	D	72	CYS	0	-0.028	-0.022	18.021	0.020	0.020	0.000	0.000	0.000
70	D	73	ASP	-1	-0.868	-0.922	13.537	-0.081	-0.081	0.000	0.000	0.000
71	D	74	ASP	-1	-0.871	-0.945	12.957	-0.369	-0.369	0.000	0.000	0.000
72	D	75	VAL	0	-0.048	-0.016	14.035	-0.043	-0.043	0.000	0.000	0.000
73	D	76	TRP	0	-0.017	-0.003	16.457	0.038	0.038	0.000	0.000	0.000
74	D	77	THR	0	-0.047	-0.028	20.082	-0.004	-0.004	0.000	0.000	0.000
75	D	78	PHE	0	-0.003	-0.009	22.181	0.009	0.009	0.000	0.000	0.000
76	D	79	ILE	0	-0.031	-0.020	25.636	0.000	0.000	0.000	0.000	0.000
77	D	80	VAL	0	0.019	0.009	28.459	0.004	0.004	0.000	0.000	0.000
78	D	81	LYS	1	0.909	0.945	31.106	0.043	0.043	0.000	0.000	0.000
79	D	82	ASN	0	-0.023	-0.009	34.542	-0.001	-0.001	0.000	0.000	0.000
80	D	83	CYS	0	-0.037	-0.013	33.003	-0.002	-0.002	0.000	0.000	0.000
81	D	84	GLN	0	0.017	0.011	35.594	0.000	0.000	0.000	0.000	0.000
82	D	85	VAL	0	-0.008	-0.023	31.097	-0.005	-0.005	0.000	0.000	0.000
83	D	86	THR	0	-0.025	-0.016	33.559	0.005	0.005	0.000	0.000	0.000
84	D	87	VAL	0	-0.012	-0.016	31.691	-0.007	-0.007	0.000	0.000	0.000
85	D	88	GLU	-1	-0.883	-0.945	32.181	-0.088	-0.088	0.000	0.000	0.000
86	D	89	NME	0	-0.038	0.004	34.026	0.001	0.001	0.000	0.000	0.000
87	D	103	ACE	0	0.046	-0.002	37.267	0.000	0.000	0.000	0.000	0.000
88	D	104	SER	0	-0.054	-0.018	36.755	0.004	0.004	0.000	0.000	0.000
89	D	105	VAL	0	0.018	0.006	36.869	-0.004	-0.004	0.000	0.000	0.000
90	D	106	ILE	0	0.012	0.012	34.174	0.003	0.003	0.000	0.000	0.000
91	D	107	SER	0	-0.022	-0.014	36.393	-0.002	-0.002	0.000	0.000	0.000
92	D	108	VAL	0	0.000	-0.003	31.896	0.001	0.001	0.000	0.000	0.000
93	D	109	ASP	-1	-0.875	-0.914	35.167	-0.039	-0.039	0.000	0.000	0.000
94	D	110	LYS	1	0.923	0.943	30.279	0.040	0.040	0.000	0.000	0.000
95	D	111	LEU	0	0.030	0.033	27.117	0.000	0.000	0.000	0.000	0.000
96	D	112	ARG	1	0.934	0.967	23.183	0.064	0.064	0.000	0.000	0.000
97	D	113	ILE	0	-0.003	-0.002	22.181	-0.004	-0.004	0.000	0.000	0.000
98	D	114	VAL	0	0.000	-0.008	17.037	0.010	0.010	0.000	0.000	0.000
99	D	115	ALA	0	-0.020	-0.006	17.723	-0.012	-0.012	0.000	0.000	0.000
100	D	116	CYS	0	0.038	0.030	11.886	0.040	0.040	0.000	0.000	0.000
101	D	117	ASN	0	0.047	0.029	13.024	0.012	0.012	0.000	0.000	0.000
102	D	118	SER	0	0.010	0.008	13.011	-0.075	-0.075	0.000	0.000	0.000
103	D	119	LYS	1	0.842	0.926	13.622	0.264	0.264	0.000	0.000	0.000
104	D	120	NME	0	0.071	0.047	9.582	0.021	0.021	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:4:ACE )