FMO DATABASE

FMODB ID: 49JVN

Calculation Name: 1YO5-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YO5

Chain ID: C

ChEMBL ID:

UniProt ID: O95238

Base Structure: X-ray

Registration Date: 2023-06-22

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-706508.631748
FMO2-HF: Nuclear repulsion	669945.161512
FMO2-HF: Total energy	-36563.470236
FMO2-MP2: Total energy	-36673.665398

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(C:247:GLN)

Summations of interaction energy for fragment #1(C:247:GLN)

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.
-23.556	-20.339	7.258	-4.971	-5.505	0.042

Interaction energy analysis for fragmet #1(C:247:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.103 / q_NPA : 0.059

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	C	249	ILE	0	0.039	0.032	2.602	-1.833	1.206	0.895	-1.787	-2.147	-0.002
4	C	250	HIS	0	0.003	-0.014	1.927	-14.884	-14.706	6.363	-3.184	-3.358	0.044
5	C	251	LEU	0	0.015	-0.002	6.443	-0.798	-0.798	0.000	0.000	0.000	0.000
6	C	252	TRP	0	0.050	0.010	7.339	-0.898	-0.898	0.000	0.000	0.000	0.000
7	C	253	GLN	0	0.046	0.033	5.758	-0.311	-0.311	0.000	0.000	0.000	0.000
8	C	254	PHE	0	0.032	0.009	9.718	-0.269	-0.269	0.000	0.000	0.000	0.000
9	C	255	LEU	0	-0.001	-0.008	11.210	-0.090	-0.090	0.000	0.000	0.000	0.000
10	C	256	LYS	1	0.901	0.951	13.193	-0.256	-0.256	0.000	0.000	0.000	0.000
11	C	257	GLU	-1	-0.806	-0.869	12.421	-1.000	-1.000	0.000	0.000	0.000	0.000
12	C	258	LEU	0	-0.034	-0.018	14.515	-0.017	-0.017	0.000	0.000	0.000	0.000
13	C	259	LEU	0	-0.019	-0.008	17.310	0.004	0.004	0.000	0.000	0.000	0.000
14	C	260	LEU	0	-0.036	-0.002	16.709	0.012	0.012	0.000	0.000	0.000	0.000
15	C	261	LYS	1	0.897	0.948	16.224	0.702	0.702	0.000	0.000	0.000	0.000
16	C	262	PRO	0	0.069	0.033	21.363	0.006	0.006	0.000	0.000	0.000	0.000
17	C	263	HIS	0	0.078	0.043	24.199	0.027	0.027	0.000	0.000	0.000	0.000
18	C	264	SER	0	0.029	0.032	21.709	0.004	0.004	0.000	0.000	0.000	0.000
19	C	265	TYR	0	-0.003	-0.021	17.459	0.021	0.021	0.000	0.000	0.000	0.000
20	C	266	GLY	0	0.021	0.022	22.583	0.037	0.037	0.000	0.000	0.000	0.000
21	C	267	ARG	1	0.852	0.909	25.253	0.172	0.172	0.000	0.000	0.000	0.000
22	C	268	PHE	0	0.007	0.002	22.234	0.014	0.014	0.000	0.000	0.000	0.000
23	C	269	ILE	0	-0.038	-0.018	18.562	0.048	0.048	0.000	0.000	0.000	0.000
24	C	270	ARG	1	0.892	0.940	22.673	-0.061	-0.061	0.000	0.000	0.000	0.000
25	C	271	TRP	0	0.001	-0.010	18.896	0.053	0.053	0.000	0.000	0.000	0.000
26	C	272	LEU	0	-0.046	-0.026	24.672	-0.013	-0.013	0.000	0.000	0.000	0.000
27	C	273	ASN	0	0.056	0.020	26.447	-0.015	-0.015	0.000	0.000	0.000	0.000
28	C	274	LYS	1	0.969	0.980	22.679	0.139	0.139	0.000	0.000	0.000	0.000
29	C	275	GLU	-1	-0.788	-0.868	23.874	0.100	0.100	0.000	0.000	0.000	0.000
30	C	276	LYS	1	0.877	0.931	24.707	-0.092	-0.092	0.000	0.000	0.000	0.000
31	C	277	GLY	0	0.051	0.037	21.484	0.043	0.043	0.000	0.000	0.000	0.000
32	C	278	ILE	0	-0.012	-0.011	21.479	0.051	0.051	0.000	0.000	0.000	0.000
33	C	279	PHE	0	0.006	0.008	18.085	-0.043	-0.043	0.000	0.000	0.000	0.000
34	C	280	LYS	1	0.897	0.921	23.167	-0.052	-0.052	0.000	0.000	0.000	0.000
35	C	281	ILE	0	-0.057	-0.033	19.595	-0.024	-0.024	0.000	0.000	0.000	0.000
36	C	282	GLU	-1	-0.753	-0.859	23.522	0.067	0.067	0.000	0.000	0.000	0.000
37	C	283	ASP	-1	-0.817	-0.900	24.678	-0.003	-0.003	0.000	0.000	0.000	0.000
38	C	284	SER	0	-0.012	-0.023	22.799	-0.014	-0.014	0.000	0.000	0.000	0.000
39	C	285	ALA	0	0.046	0.022	22.082	0.018	0.018	0.000	0.000	0.000	0.000
40	C	286	GLN	0	0.066	0.046	22.416	-0.021	-0.021	0.000	0.000	0.000	0.000
41	C	287	VAL	0	-0.030	-0.013	17.727	-0.033	-0.033	0.000	0.000	0.000	0.000
42	C	288	ALA	0	-0.034	-0.022	17.626	-0.008	-0.008	0.000	0.000	0.000	0.000
43	C	289	ARG	1	0.960	0.978	17.878	0.186	0.186	0.000	0.000	0.000	0.000
44	C	290	LEU	0	-0.013	-0.008	16.975	-0.052	-0.052	0.000	0.000	0.000	0.000
45	C	291	TRP	0	0.008	-0.002	8.528	-0.073	-0.073	0.000	0.000	0.000	0.000
46	C	292	GLY	0	0.017	-0.002	13.333	-0.051	-0.051	0.000	0.000	0.000	0.000
47	C	293	ILE	0	0.017	0.013	14.901	-0.051	-0.051	0.000	0.000	0.000	0.000
48	C	294	ARG	1	0.814	0.900	9.889	1.063	1.063	0.000	0.000	0.000	0.000
49	C	295	LYS	1	0.810	0.907	6.828	-0.905	-0.905	0.000	0.000	0.000	0.000
50	C	296	ASN	0	0.046	0.038	10.952	0.110	0.110	0.000	0.000	0.000	0.000
51	C	297	ARG	1	0.887	0.937	11.437	-0.120	-0.120	0.000	0.000	0.000	0.000
52	C	298	PRO	0	0.092	0.042	15.419	0.037	0.037	0.000	0.000	0.000	0.000
53	C	299	ALA	0	0.043	0.033	18.852	0.014	0.014	0.000	0.000	0.000	0.000
54	C	300	MET	0	-0.105	-0.027	14.310	0.084	0.084	0.000	0.000	0.000	0.000
55	C	301	ASN	0	0.061	0.004	18.579	-0.002	-0.002	0.000	0.000	0.000	0.000
56	C	302	TYR	0	0.111	0.040	19.682	0.069	0.069	0.000	0.000	0.000	0.000
57	C	303	ASP	-1	-0.815	-0.888	20.942	0.325	0.325	0.000	0.000	0.000	0.000
58	C	304	LYS	1	0.888	0.932	17.815	-0.235	-0.235	0.000	0.000	0.000	0.000
59	C	305	LEU	0	0.008	0.015	15.484	0.118	0.118	0.000	0.000	0.000	0.000
60	C	306	SER	0	-0.009	-0.009	16.626	0.124	0.124	0.000	0.000	0.000	0.000
61	C	307	ARG	1	0.878	0.931	18.074	-0.795	-0.795	0.000	0.000	0.000	0.000
62	C	308	SER	0	0.001	-0.005	13.045	0.137	0.137	0.000	0.000	0.000	0.000
63	C	309	ILE	0	-0.003	0.003	14.311	0.163	0.163	0.000	0.000	0.000	0.000
64	C	310	ARG	1	0.939	0.968	16.139	-0.486	-0.486	0.000	0.000	0.000	0.000
65	C	311	GLN	0	0.003	0.020	13.994	-0.131	-0.131	0.000	0.000	0.000	0.000
66	C	312	TYR	0	-0.007	-0.018	8.961	-0.026	-0.026	0.000	0.000	0.000	0.000
67	C	313	TYR	0	0.044	0.019	14.685	-0.045	-0.045	0.000	0.000	0.000	0.000
68	C	314	LYS	1	0.978	0.987	16.668	-0.968	-0.968	0.000	0.000	0.000	0.000
69	C	315	LYS	1	0.916	0.966	11.117	-1.967	-1.967	0.000	0.000	0.000	0.000
70	C	316	GLY	0	0.071	0.057	14.864	0.012	0.012	0.000	0.000	0.000	0.000
71	C	317	ILE	0	-0.027	-0.010	10.310	-0.021	-0.021	0.000	0.000	0.000	0.000
72	C	318	ILE	0	-0.043	-0.031	14.557	-0.129	-0.129	0.000	0.000	0.000	0.000
73	C	319	ARG	1	0.818	0.867	17.061	-0.270	-0.270	0.000	0.000	0.000	0.000
74	C	320	LYS	1	0.826	0.913	20.629	-0.367	-0.367	0.000	0.000	0.000	0.000
75	C	321	PRO	0	0.004	0.001	23.868	0.007	0.007	0.000	0.000	0.000	0.000
76	C	322	ASP	-1	-0.795	-0.869	26.333	0.261	0.261	0.000	0.000	0.000	0.000
77	C	323	ILE	0	0.044	0.045	29.343	0.001	0.001	0.000	0.000	0.000	0.000
78	C	324	SER	0	-0.014	-0.016	28.299	0.002	0.002	0.000	0.000	0.000	0.000
79	C	325	GLN	0	0.061	0.024	28.283	-0.030	-0.030	0.000	0.000	0.000	0.000
80	C	326	ARG	1	0.976	0.966	27.532	-0.145	-0.145	0.000	0.000	0.000	0.000
81	C	327	LEU	0	-0.024	-0.009	24.706	-0.013	-0.013	0.000	0.000	0.000	0.000
82	C	328	VAL	0	0.034	0.042	24.473	-0.011	-0.011	0.000	0.000	0.000	0.000
83	C	329	TYR	0	-0.051	-0.032	20.261	0.062	0.062	0.000	0.000	0.000	0.000
84	C	330	GLN	0	0.050	0.026	21.202	-0.038	-0.038	0.000	0.000	0.000	0.000
85	C	331	PHE	0	-0.035	-0.029	14.451	0.076	0.076	0.000	0.000	0.000	0.000
86	C	332	VAL	0	-0.015	0.005	17.539	-0.054	-0.054	0.000	0.000	0.000	0.000
87	C	333	HIS	0	0.099	0.055	15.466	-0.121	-0.121	0.000	0.000	0.000	0.000
88	C	334	PRO	0	-0.026	-0.002	16.157	-0.084	-0.084	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:247:GLN)