FMO DATABASE

FMODB ID: 6YL6Z

Calculation Name: 1YD8-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YD8

Chain ID: G

ChEMBL ID:

UniProt ID: Q9NZ52

Base Structure: X-ray

Registration Date: 2023-09-20

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-650959.734861
FMO2-HF: Nuclear repulsion	612997.624488
FMO2-HF: Total energy	-37962.110373
FMO2-MP2: Total energy	-38072.037467

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(G:-1:GLY)

Summations of interaction energy for fragment #1(G:-1: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.
-9.558	-6.847	1.845	-1.931	-2.625	0.01

Interaction energy analysis for fragmet #1(G:-1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.003

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	G	209	GLN	0	0.053	0.014	3.865	0.551	1.854	-0.012	-0.655	-0.636	-0.001
4	G	210	LYS	1	0.955	0.976	2.398	-6.724	-5.486	1.857	-1.239	-1.855	0.011
5	G	211	VAL	0	0.092	0.056	3.845	-1.280	-1.110	0.000	-0.037	-0.134	0.000
6	G	212	THR	0	0.050	0.025	5.612	-0.030	-0.030	0.000	0.000	0.000	0.000
7	G	213	LYS	1	0.952	0.974	7.606	-1.363	-1.363	0.000	0.000	0.000	0.000
8	G	214	ARG	1	0.965	0.989	7.770	-0.507	-0.507	0.000	0.000	0.000	0.000
9	G	215	LEU	0	0.077	0.048	9.405	-0.074	-0.074	0.000	0.000	0.000	0.000
10	G	216	HIS	0	-0.013	-0.018	11.612	0.007	0.007	0.000	0.000	0.000	0.000
11	G	217	THR	0	-0.041	-0.026	12.405	-0.024	-0.024	0.000	0.000	0.000	0.000
12	G	218	LEU	0	0.021	0.008	12.805	-0.033	-0.033	0.000	0.000	0.000	0.000
13	G	219	GLU	-1	-0.895	-0.946	15.528	0.033	0.033	0.000	0.000	0.000	0.000
14	G	220	GLU	-1	-0.872	-0.905	17.167	0.255	0.255	0.000	0.000	0.000	0.000
15	G	221	VAL	0	-0.040	-0.018	18.422	-0.012	-0.012	0.000	0.000	0.000	0.000
16	G	222	ASN	0	0.038	0.017	19.700	-0.020	-0.020	0.000	0.000	0.000	0.000
17	G	223	ASN	0	0.006	-0.019	20.686	-0.018	-0.018	0.000	0.000	0.000	0.000
18	G	224	ASN	0	0.025	0.020	23.188	0.005	0.005	0.000	0.000	0.000	0.000
19	G	225	VAL	0	0.016	0.007	23.738	-0.007	-0.007	0.000	0.000	0.000	0.000
20	G	226	ARG	1	0.886	0.959	23.104	-0.031	-0.031	0.000	0.000	0.000	0.000
21	G	227	LEU	0	0.075	0.043	27.528	-0.003	-0.003	0.000	0.000	0.000	0.000
22	G	228	LEU	0	0.029	0.013	29.065	-0.004	-0.004	0.000	0.000	0.000	0.000
23	G	229	SER	0	-0.048	-0.048	29.615	-0.006	-0.006	0.000	0.000	0.000	0.000
24	G	230	GLU	-1	-0.952	-0.974	31.593	0.034	0.034	0.000	0.000	0.000	0.000
25	G	231	MET	0	0.001	-0.004	33.429	-0.001	-0.001	0.000	0.000	0.000	0.000
26	G	232	LEU	0	-0.043	-0.022	33.551	-0.002	-0.002	0.000	0.000	0.000	0.000
27	G	233	LEU	0	-0.057	-0.033	35.314	-0.003	-0.003	0.000	0.000	0.000	0.000
28	G	234	HIS	0	-0.110	-0.048	36.914	-0.006	-0.006	0.000	0.000	0.000	0.000
29	G	235	TYR	0	-0.014	-0.006	39.576	0.003	0.003	0.000	0.000	0.000	0.000
30	G	236	SER	0	-0.019	-0.033	41.405	-0.002	-0.002	0.000	0.000	0.000	0.000
31	G	237	GLN	0	-0.017	0.007	45.026	0.004	0.004	0.000	0.000	0.000	0.000
32	G	238	GLU	-1	-0.869	-0.911	47.077	0.024	0.024	0.000	0.000	0.000	0.000
33	G	239	ASP	-1	-0.969	-0.986	46.781	0.025	0.025	0.000	0.000	0.000	0.000
34	G	240	SER	0	0.028	0.001	42.227	0.002	0.002	0.000	0.000	0.000	0.000
35	G	241	SER	0	-0.059	-0.043	43.070	0.001	0.001	0.000	0.000	0.000	0.000
36	G	242	ASP	-1	-0.890	-0.972	43.105	0.043	0.043	0.000	0.000	0.000	0.000
37	G	243	GLY	0	-0.002	-0.006	40.721	0.003	0.003	0.000	0.000	0.000	0.000
38	G	244	ASP	-1	-0.840	-0.882	38.886	0.046	0.046	0.000	0.000	0.000	0.000
39	G	245	ARG	1	0.862	0.912	37.927	-0.034	-0.034	0.000	0.000	0.000	0.000
40	G	246	GLU	-1	-1.011	-1.006	37.939	0.071	0.071	0.000	0.000	0.000	0.000
41	G	247	LEU	0	0.097	0.062	32.589	0.005	0.005	0.000	0.000	0.000	0.000
42	G	248	MET	0	-0.036	-0.011	33.556	0.005	0.005	0.000	0.000	0.000	0.000
43	G	249	LYS	1	0.911	0.960	33.523	-0.049	-0.049	0.000	0.000	0.000	0.000
44	G	250	GLU	-1	-0.925	-0.950	31.221	0.105	0.105	0.000	0.000	0.000	0.000
45	G	251	LEU	0	-0.002	-0.008	27.684	0.010	0.010	0.000	0.000	0.000	0.000
46	G	252	PHE	0	-0.003	-0.010	28.742	0.006	0.006	0.000	0.000	0.000	0.000
47	G	253	ASP	-1	-0.879	-0.914	29.530	0.115	0.115	0.000	0.000	0.000	0.000
48	G	254	GLN	0	-0.020	-0.026	24.455	0.007	0.007	0.000	0.000	0.000	0.000
49	G	255	CYS	0	-0.039	-0.015	24.883	0.012	0.012	0.000	0.000	0.000	0.000
50	G	256	GLU	-1	-0.727	-0.866	25.226	0.082	0.082	0.000	0.000	0.000	0.000
51	G	257	ASN	0	-0.058	-0.038	24.844	0.002	0.002	0.000	0.000	0.000	0.000
52	G	258	LYS	1	0.806	0.886	19.133	-0.194	-0.194	0.000	0.000	0.000	0.000
53	G	259	ARG	1	0.813	0.908	20.541	-0.073	-0.073	0.000	0.000	0.000	0.000
54	G	260	ARG	1	0.881	0.938	21.952	-0.134	-0.134	0.000	0.000	0.000	0.000
55	G	261	THR	0	-0.027	-0.019	16.989	0.004	0.004	0.000	0.000	0.000	0.000
56	G	262	LEU	0	-0.035	-0.007	16.146	0.029	0.029	0.000	0.000	0.000	0.000
57	G	263	PHE	0	0.026	0.004	17.661	-0.007	-0.007	0.000	0.000	0.000	0.000
58	G	264	LYS	1	0.922	0.986	16.447	-0.340	-0.340	0.000	0.000	0.000	0.000
59	G	265	LEU	0	-0.001	0.001	12.108	0.023	0.023	0.000	0.000	0.000	0.000
60	G	266	ALA	0	-0.005	0.013	13.735	-0.012	-0.012	0.000	0.000	0.000	0.000
61	G	267	SER	0	-0.085	-0.054	16.115	-0.020	-0.020	0.000	0.000	0.000	0.000
62	G	268	GLU	-1	-0.955	-0.986	12.670	0.385	0.385	0.000	0.000	0.000	0.000
63	G	269	THR	0	-0.084	-0.046	10.696	0.015	0.015	0.000	0.000	0.000	0.000
64	G	270	GLU	-1	-0.886	-0.952	11.261	-0.001	-0.001	0.000	0.000	0.000	0.000
65	G	271	ASP	-1	-0.941	-0.976	13.492	-0.133	-0.133	0.000	0.000	0.000	0.000
66	G	272	ASN	0	-0.080	-0.029	9.171	-0.097	-0.097	0.000	0.000	0.000	0.000
67	G	273	ASP	-1	-0.818	-0.913	13.377	-0.231	-0.231	0.000	0.000	0.000	0.000
68	G	274	ASN	0	-0.091	-0.036	11.983	-0.092	-0.092	0.000	0.000	0.000	0.000
69	G	275	SER	0	0.038	0.018	9.869	0.084	0.084	0.000	0.000	0.000	0.000
70	G	276	LEU	0	0.004	0.009	11.900	0.069	0.069	0.000	0.000	0.000	0.000
71	G	277	GLY	0	0.036	0.014	15.125	0.028	0.028	0.000	0.000	0.000	0.000
72	G	278	ASP	-1	-0.903	-0.961	13.078	-0.130	-0.130	0.000	0.000	0.000	0.000
73	G	279	ILE	0	-0.058	-0.033	12.048	0.038	0.038	0.000	0.000	0.000	0.000
74	G	280	LEU	0	0.019	0.009	16.108	0.016	0.016	0.000	0.000	0.000	0.000
75	G	281	GLN	0	0.006	0.020	19.179	0.010	0.010	0.000	0.000	0.000	0.000
76	G	282	ALA	0	0.013	0.006	18.178	0.005	0.005	0.000	0.000	0.000	0.000
77	G	283	SER	0	-0.034	-0.036	20.080	0.007	0.007	0.000	0.000	0.000	0.000
78	G	284	ASP	-1	-0.815	-0.870	21.963	0.012	0.012	0.000	0.000	0.000	0.000
79	G	285	ASN	0	-0.022	-0.018	23.280	0.000	0.000	0.000	0.000	0.000	0.000
80	G	286	LEU	0	0.017	0.010	21.833	0.001	0.001	0.000	0.000	0.000	0.000
81	G	287	SER	0	-0.027	-0.028	25.450	0.001	0.001	0.000	0.000	0.000	0.000
82	G	288	ARG	1	0.800	0.872	27.889	-0.013	-0.013	0.000	0.000	0.000	0.000
83	G	289	VAL	0	0.020	0.021	28.576	-0.002	-0.002	0.000	0.000	0.000	0.000
84	G	290	ILE	0	-0.035	-0.009	26.827	0.000	0.000	0.000	0.000	0.000	0.000
85	G	291	ASN	0	0.013	-0.010	30.900	0.004	0.004	0.000	0.000	0.000	0.000
86	G	292	SER	0	-0.007	0.010	33.378	-0.002	-0.002	0.000	0.000	0.000	0.000
87	G	293	TYR	0	0.087	0.025	33.660	-0.002	-0.002	0.000	0.000	0.000	0.000
88	G	294	LYS	1	0.801	0.924	32.805	-0.058	-0.058	0.000	0.000	0.000	0.000
89	G	295	THR	0	-0.015	-0.019	37.562	-0.003	-0.003	0.000	0.000	0.000	0.000
90	G	296	ILE	0	-0.006	0.000	37.135	-0.002	-0.002	0.000	0.000	0.000	0.000
91	G	297	ILE	0	-0.041	-0.016	38.050	0.000	0.000	0.000	0.000	0.000	0.000
92	G	298	GLU	-1	-0.958	-0.978	40.457	0.037	0.037	0.000	0.000	0.000	0.000
93	G	299	GLY	0	-0.085	-0.031	42.899	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:-1:GLY)