FMO DATABASE

FMODB ID: 89L2Y

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	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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-637646.571289
FMO2-HF: Nuclear repulsion	598054.412132
FMO2-HF: Total energy	-39592.159157
FMO2-MP2: Total energy	-39706.292374

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.
-3.571	-2.371	-0.008	-0.791	-0.402	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 : 0.025 / 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

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	0.008	0.002	3.816	-1.490	-0.290	-0.008	-0.791	-0.402	0.004
4	D	8	GLU	-1	-0.866	-0.932	6.381	-1.929	-1.929	0.000	0.000	0.000	0.000
5	D	9	LEU	0	-0.048	-0.035	9.094	0.416	0.416	0.000	0.000	0.000	0.000
6	D	10	TYR	0	0.036	0.004	10.384	0.220	0.220	0.000	0.000	0.000	0.000
7	D	11	ARG	1	0.886	0.938	8.805	2.055	2.055	0.000	0.000	0.000	0.000
8	D	12	ARG	1	0.934	0.973	14.649	0.723	0.723	0.000	0.000	0.000	0.000
9	D	13	SER	0	-0.036	-0.020	16.549	0.111	0.111	0.000	0.000	0.000	0.000
10	D	14	THR	0	0.037	0.010	18.655	-0.010	-0.010	0.000	0.000	0.000	0.000
11	D	15	ILE	0	0.022	0.011	17.548	0.011	0.011	0.000	0.000	0.000	0.000
12	D	16	GLY	0	0.005	0.005	16.774	-0.014	-0.014	0.000	0.000	0.000	0.000
13	D	17	ASN	0	-0.001	-0.010	17.450	-0.023	-0.023	0.000	0.000	0.000	0.000
14	D	18	SER	0	0.009	0.006	20.129	0.031	0.031	0.000	0.000	0.000	0.000
15	D	19	LEU	0	-0.043	-0.004	15.502	0.024	0.024	0.000	0.000	0.000	0.000
16	D	20	VAL	0	-0.013	-0.012	16.833	-0.001	-0.001	0.000	0.000	0.000	0.000
17	D	21	ASP	-1	-0.843	-0.919	19.106	-0.372	-0.372	0.000	0.000	0.000	0.000
18	D	22	ALA	0	-0.051	-0.020	21.907	0.035	0.035	0.000	0.000	0.000	0.000
19	D	23	LEU	0	-0.037	-0.039	16.822	0.027	0.027	0.000	0.000	0.000	0.000
20	D	24	ASP	-1	-0.880	-0.938	20.812	-0.441	-0.441	0.000	0.000	0.000	0.000
21	D	25	THR	0	-0.048	-0.026	22.713	0.042	0.042	0.000	0.000	0.000	0.000
22	D	26	LEU	0	-0.005	-0.014	22.835	0.024	0.024	0.000	0.000	0.000	0.000
23	D	27	ILE	0	-0.051	-0.023	19.969	0.017	0.017	0.000	0.000	0.000	0.000
24	D	28	SER	0	-0.068	-0.038	24.538	0.026	0.026	0.000	0.000	0.000	0.000
25	D	29	ASP	-1	-0.979	-0.978	27.461	-0.191	-0.191	0.000	0.000	0.000	0.000
26	D	30	GLY	0	-0.028	0.005	28.371	0.018	0.018	0.000	0.000	0.000	0.000
27	D	31	ARG	1	0.932	0.954	28.079	0.176	0.176	0.000	0.000	0.000	0.000
28	D	32	ILE	0	-0.050	-0.021	22.706	0.009	0.009	0.000	0.000	0.000	0.000
29	D	33	GLU	-1	-0.905	-0.961	21.215	-0.237	-0.237	0.000	0.000	0.000	0.000
30	D	34	ALA	0	0.103	0.065	20.027	-0.042	-0.042	0.000	0.000	0.000	0.000
31	D	35	SER	0	-0.023	-0.001	16.244	0.015	0.015	0.000	0.000	0.000	0.000
32	D	36	LEU	0	-0.044	-0.035	15.132	-0.083	-0.083	0.000	0.000	0.000	0.000
33	D	37	ALA	0	0.052	0.019	15.610	-0.073	-0.073	0.000	0.000	0.000	0.000
34	D	38	MET	0	0.006	0.006	10.237	-0.032	-0.032	0.000	0.000	0.000	0.000
35	D	39	ARG	1	0.993	0.995	11.479	0.316	0.316	0.000	0.000	0.000	0.000
36	D	40	VAL	0	-0.008	0.000	11.642	-0.132	-0.132	0.000	0.000	0.000	0.000
37	D	41	LEU	0	0.009	-0.003	11.844	-0.086	-0.086	0.000	0.000	0.000	0.000
38	D	42	GLU	-1	-0.887	-0.937	7.448	-1.771	-1.771	0.000	0.000	0.000	0.000
39	D	43	THR	0	-0.096	-0.050	8.144	-0.259	-0.259	0.000	0.000	0.000	0.000
40	D	44	PHE	0	-0.039	-0.018	10.692	0.039	0.039	0.000	0.000	0.000	0.000
41	D	45	ASP	-1	-0.734	-0.860	7.251	-2.474	-2.474	0.000	0.000	0.000	0.000
42	D	46	LYS	1	0.919	0.971	7.160	0.874	0.874	0.000	0.000	0.000	0.000
43	D	47	VAL	0	0.032	0.013	8.166	0.314	0.314	0.000	0.000	0.000	0.000
44	D	48	VAL	0	-0.020	-0.003	11.890	0.179	0.179	0.000	0.000	0.000	0.000
45	D	49	ALA	0	-0.010	-0.003	8.528	0.162	0.162	0.000	0.000	0.000	0.000
46	D	50	GLU	-1	-0.931	-0.983	9.634	-0.351	-0.351	0.000	0.000	0.000	0.000
47	D	51	THR	0	0.021	0.019	11.880	0.131	0.131	0.000	0.000	0.000	0.000
48	D	52	LEU	0	-0.063	-0.034	13.690	0.091	0.091	0.000	0.000	0.000	0.000
49	D	53	LYS	1	0.793	0.920	10.811	0.243	0.243	0.000	0.000	0.000	0.000
50	D	54	ASP	-1	-0.861	-0.929	14.644	-0.134	-0.134	0.000	0.000	0.000	0.000
51	D	55	ASN	0	-0.078	-0.044	17.117	0.002	0.002	0.000	0.000	0.000	0.000
52	D	56	THR	0	-0.043	-0.026	18.112	0.007	0.007	0.000	0.000	0.000	0.000
53	D	57	GLN	0	-0.004	-0.009	20.830	0.014	0.014	0.000	0.000	0.000	0.000
54	D	58	SER	0	0.002	-0.002	23.920	0.014	0.014	0.000	0.000	0.000	0.000
55	D	59	LYS	1	0.982	1.022	23.374	0.080	0.080	0.000	0.000	0.000	0.000
56	D	60	LEU	0	0.006	-0.004	23.470	0.003	0.003	0.000	0.000	0.000	0.000
57	D	61	THR	0	-0.056	-0.025	25.672	0.013	0.013	0.000	0.000	0.000	0.000
58	D	62	VAL	0	0.021	0.012	25.166	-0.003	-0.003	0.000	0.000	0.000	0.000
59	D	63	LYS	1	0.956	0.977	28.066	0.078	0.078	0.000	0.000	0.000	0.000
60	D	64	GLY	0	0.045	0.016	31.022	-0.004	-0.004	0.000	0.000	0.000	0.000
61	D	65	ASN	0	0.006	0.023	32.178	0.010	0.010	0.000	0.000	0.000	0.000
62	D	66	LEU	0	-0.004	-0.007	26.109	-0.012	-0.012	0.000	0.000	0.000	0.000
63	D	67	ASP	-1	-0.914	-0.958	29.655	-0.115	-0.115	0.000	0.000	0.000	0.000
64	D	68	THR	0	-0.016	-0.017	25.610	0.003	0.003	0.000	0.000	0.000	0.000
65	D	69	TYR	0	-0.024	-0.013	24.176	-0.013	-0.013	0.000	0.000	0.000	0.000
66	D	70	GLY	0	0.020	0.006	22.422	0.007	0.007	0.000	0.000	0.000	0.000
67	D	71	PHE	0	-0.019	-0.010	15.513	-0.022	-0.022	0.000	0.000	0.000	0.000
68	D	72	CYS	0	-0.026	-0.021	17.392	0.037	0.037	0.000	0.000	0.000	0.000
69	D	73	ASP	-1	-0.865	-0.920	13.035	-0.143	-0.143	0.000	0.000	0.000	0.000
70	D	74	ASP	-1	-0.874	-0.947	10.808	0.128	0.128	0.000	0.000	0.000	0.000
71	D	75	VAL	0	-0.047	-0.016	12.011	-0.092	-0.092	0.000	0.000	0.000	0.000
72	D	76	TRP	0	-0.018	-0.003	14.320	0.045	0.045	0.000	0.000	0.000	0.000
73	D	77	THR	0	-0.048	-0.029	17.549	-0.067	-0.067	0.000	0.000	0.000	0.000
74	D	78	PHE	0	-0.007	-0.010	19.744	0.035	0.035	0.000	0.000	0.000	0.000
75	D	79	ILE	0	-0.024	-0.018	23.111	-0.029	-0.029	0.000	0.000	0.000	0.000
76	D	80	VAL	0	0.014	0.007	25.821	0.018	0.018	0.000	0.000	0.000	0.000
77	D	81	LYS	1	0.914	0.948	28.347	0.121	0.121	0.000	0.000	0.000	0.000
78	D	82	ASN	0	-0.026	-0.010	31.883	0.002	0.002	0.000	0.000	0.000	0.000
79	D	83	CYS	0	-0.039	-0.014	29.935	0.002	0.002	0.000	0.000	0.000	0.000
80	D	84	GLN	0	0.019	0.012	32.429	-0.001	-0.001	0.000	0.000	0.000	0.000
81	D	85	VAL	0	-0.012	-0.025	27.608	0.000	0.000	0.000	0.000	0.000	0.000
82	D	86	THR	0	-0.026	-0.017	29.791	0.007	0.007	0.000	0.000	0.000	0.000
83	D	87	VAL	0	-0.025	-0.017	27.847	-0.006	-0.006	0.000	0.000	0.000	0.000
84	D	88	GLU	-1	-0.907	-0.950	28.161	-0.102	-0.102	0.000	0.000	0.000	0.000
85	D	104	SER	0	0.046	0.033	32.978	0.003	0.003	0.000	0.000	0.000	0.000
86	D	105	VAL	0	-0.024	-0.031	33.096	-0.004	-0.004	0.000	0.000	0.000	0.000
87	D	106	ILE	0	0.008	0.010	30.656	0.001	0.001	0.000	0.000	0.000	0.000
88	D	107	SER	0	-0.022	-0.014	33.012	0.006	0.006	0.000	0.000	0.000	0.000
89	D	108	VAL	0	0.001	-0.003	29.115	-0.007	-0.007	0.000	0.000	0.000	0.000
90	D	109	ASP	-1	-0.873	-0.914	32.283	-0.123	-0.123	0.000	0.000	0.000	0.000
91	D	110	LYS	1	0.922	0.943	28.418	0.184	0.184	0.000	0.000	0.000	0.000
92	D	111	LEU	0	0.028	0.033	24.178	-0.012	-0.012	0.000	0.000	0.000	0.000
93	D	112	ARG	1	0.934	0.966	21.403	0.293	0.293	0.000	0.000	0.000	0.000
94	D	113	ILE	0	-0.001	-0.001	19.123	-0.022	-0.022	0.000	0.000	0.000	0.000
95	D	114	VAL	0	0.001	-0.008	14.625	0.021	0.021	0.000	0.000	0.000	0.000
96	D	115	ALA	0	-0.018	-0.005	14.532	-0.046	-0.046	0.000	0.000	0.000	0.000
97	D	116	CYS	0	0.037	0.030	9.337	0.052	0.052	0.000	0.000	0.000	0.000
98	D	117	ASN	0	0.046	0.028	9.840	0.034	0.034	0.000	0.000	0.000	0.000
99	D	118	SER	0	0.011	0.011	9.230	-0.046	-0.046	0.000	0.000	0.000	0.000
100	D	119	LYS	1	0.913	0.970	7.671	-0.106	-0.106	0.000	0.000	0.000	0.000

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