FMO DATABASE

FMODB ID: 763GK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-652356.457159
FMO2-HF: Nuclear repulsion	614396.79323
FMO2-HF: Total energy	-37959.663929
FMO2-MP2: Total energy	-38069.971736

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.
-9.078	-10.972	9.251	-3.825	-3.532	0.02

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 : 0.033 / 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

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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	0.100	0.028	3.797	0.358	1.282	-0.009	-0.425	-0.491	0.001
4	G	210	LYS	1	0.872	0.930	1.970	-5.020	-8.211	9.258	-3.355	-2.712	0.019
5	G	211	VAL	0	0.096	0.054	3.641	-1.952	-1.629	0.003	-0.042	-0.284	0.000
6	G	212	THR	0	0.055	0.027	4.906	-0.074	-0.024	-0.001	-0.003	-0.045	0.000
7	G	213	LYS	1	0.936	0.963	7.015	-1.731	-1.731	0.000	0.000	0.000	0.000
8	G	214	ARG	1	0.993	1.012	7.102	-0.319	-0.319	0.000	0.000	0.000	0.000
9	G	215	LEU	0	0.098	0.046	8.642	-0.032	-0.032	0.000	0.000	0.000	0.000
10	G	216	HIS	0	-0.032	-0.028	10.682	0.004	0.004	0.000	0.000	0.000	0.000
11	G	217	THR	0	-0.066	-0.042	11.885	-0.017	-0.017	0.000	0.000	0.000	0.000
12	G	218	LEU	0	0.001	0.003	11.332	-0.030	-0.030	0.000	0.000	0.000	0.000
13	G	219	GLU	-1	-0.867	-0.929	14.799	0.006	0.006	0.000	0.000	0.000	0.000
14	G	220	GLU	-1	-0.947	-0.972	16.711	0.209	0.209	0.000	0.000	0.000	0.000
15	G	221	VAL	0	-0.096	-0.077	17.145	-0.011	-0.011	0.000	0.000	0.000	0.000
16	G	222	ASN	0	0.054	0.010	19.209	-0.007	-0.007	0.000	0.000	0.000	0.000
17	G	223	ASN	0	0.026	0.015	20.253	-0.024	-0.024	0.000	0.000	0.000	0.000
18	G	224	ASN	0	0.011	0.018	22.635	0.000	0.000	0.000	0.000	0.000	0.000
19	G	225	VAL	0	0.011	0.011	23.872	-0.006	-0.006	0.000	0.000	0.000	0.000
20	G	226	ARG	1	0.902	0.948	24.835	-0.011	-0.011	0.000	0.000	0.000	0.000
21	G	227	LEU	0	0.054	0.028	26.891	-0.002	-0.002	0.000	0.000	0.000	0.000
22	G	228	LEU	0	0.032	0.011	28.576	-0.001	-0.001	0.000	0.000	0.000	0.000
23	G	229	SER	0	-0.047	-0.036	29.492	-0.004	-0.004	0.000	0.000	0.000	0.000
24	G	230	GLU	-1	-0.928	-0.958	31.368	0.026	0.026	0.000	0.000	0.000	0.000
25	G	231	MET	0	0.022	0.002	33.025	0.000	0.000	0.000	0.000	0.000	0.000
26	G	232	LEU	0	-0.062	-0.032	33.302	-0.001	-0.001	0.000	0.000	0.000	0.000
27	G	233	LEU	0	-0.021	-0.007	34.622	-0.002	-0.002	0.000	0.000	0.000	0.000
28	G	234	HIS	0	-0.104	-0.036	36.662	-0.004	-0.004	0.000	0.000	0.000	0.000
29	G	235	TYR	0	-0.010	-0.004	39.062	0.003	0.003	0.000	0.000	0.000	0.000
30	G	236	SER	0	0.020	0.004	40.776	-0.002	-0.002	0.000	0.000	0.000	0.000
31	G	237	GLN	0	-0.023	-0.018	44.384	0.002	0.002	0.000	0.000	0.000	0.000
32	G	238	GLU	-1	-0.943	-0.960	46.535	0.017	0.017	0.000	0.000	0.000	0.000
33	G	239	ASP	-1	-1.002	-1.000	46.001	0.019	0.019	0.000	0.000	0.000	0.000
34	G	240	SER	0	0.097	0.031	42.449	0.001	0.001	0.000	0.000	0.000	0.000
35	G	241	SER	0	-0.070	-0.017	42.599	0.001	0.001	0.000	0.000	0.000	0.000
36	G	242	ASP	-1	-0.916	-0.982	42.828	0.035	0.035	0.000	0.000	0.000	0.000
37	G	243	GLY	0	0.005	-0.021	40.056	0.002	0.002	0.000	0.000	0.000	0.000
38	G	244	ASP	-1	-0.858	-0.922	38.254	0.037	0.037	0.000	0.000	0.000	0.000
39	G	245	ARG	1	0.976	0.978	37.354	-0.030	-0.030	0.000	0.000	0.000	0.000
40	G	246	GLU	-1	-0.982	-0.987	36.290	0.062	0.062	0.000	0.000	0.000	0.000
41	G	247	LEU	0	0.126	0.081	32.052	0.003	0.003	0.000	0.000	0.000	0.000
42	G	248	MET	0	-0.057	-0.001	33.194	0.004	0.004	0.000	0.000	0.000	0.000
43	G	249	LYS	1	0.874	0.934	32.704	-0.037	-0.037	0.000	0.000	0.000	0.000
44	G	250	GLU	-1	-0.871	-0.914	31.209	0.086	0.086	0.000	0.000	0.000	0.000
45	G	251	LEU	0	-0.059	-0.060	27.988	0.008	0.008	0.000	0.000	0.000	0.000
46	G	252	PHE	0	-0.083	-0.040	28.297	0.003	0.003	0.000	0.000	0.000	0.000
47	G	253	ASP	-1	-0.846	-0.912	29.072	0.079	0.079	0.000	0.000	0.000	0.000
48	G	254	GLN	0	-0.098	-0.049	24.556	0.007	0.007	0.000	0.000	0.000	0.000
49	G	255	CYS	0	-0.033	-0.026	24.424	0.011	0.011	0.000	0.000	0.000	0.000
50	G	256	GLU	-1	-0.931	-0.972	24.639	0.063	0.063	0.000	0.000	0.000	0.000
51	G	257	ASN	0	0.010	0.006	23.613	-0.006	-0.006	0.000	0.000	0.000	0.000
52	G	258	LYS	1	0.892	1.001	19.505	-0.125	-0.125	0.000	0.000	0.000	0.000
53	G	259	ARG	1	0.909	0.979	19.944	-0.056	-0.056	0.000	0.000	0.000	0.000
54	G	260	ARG	1	0.918	0.933	21.346	-0.108	-0.108	0.000	0.000	0.000	0.000
55	G	261	THR	0	-0.072	-0.034	16.199	0.012	0.012	0.000	0.000	0.000	0.000
56	G	262	LEU	0	-0.036	-0.013	15.805	0.017	0.017	0.000	0.000	0.000	0.000
57	G	263	PHE	0	0.041	0.015	17.319	-0.017	-0.017	0.000	0.000	0.000	0.000
58	G	264	LYS	1	0.956	1.001	16.341	-0.239	-0.239	0.000	0.000	0.000	0.000
59	G	265	LEU	0	-0.001	0.000	11.898	0.021	0.021	0.000	0.000	0.000	0.000
60	G	266	ALA	0	0.011	0.027	13.537	-0.026	-0.026	0.000	0.000	0.000	0.000
61	G	267	SER	0	-0.135	-0.086	15.798	-0.014	-0.014	0.000	0.000	0.000	0.000
62	G	268	GLU	-1	-1.000	-0.992	12.880	0.309	0.309	0.000	0.000	0.000	0.000
63	G	269	THR	0	-0.048	-0.049	11.326	-0.001	-0.001	0.000	0.000	0.000	0.000
64	G	270	GLU	-1	-0.933	-0.954	11.964	-0.049	-0.049	0.000	0.000	0.000	0.000
65	G	271	ASP	-1	-0.971	-0.994	13.824	-0.172	-0.172	0.000	0.000	0.000	0.000
66	G	272	ASN	0	-0.021	-0.001	9.195	-0.077	-0.077	0.000	0.000	0.000	0.000
67	G	273	ASP	-1	-0.874	-0.938	13.299	-0.254	-0.254	0.000	0.000	0.000	0.000
68	G	274	ASN	0	-0.042	-0.045	11.671	-0.069	-0.069	0.000	0.000	0.000	0.000
69	G	275	SER	0	0.038	0.045	9.976	0.061	0.061	0.000	0.000	0.000	0.000
70	G	276	LEU	0	0.032	0.031	11.640	0.067	0.067	0.000	0.000	0.000	0.000
71	G	277	GLY	0	0.032	0.025	15.029	0.031	0.031	0.000	0.000	0.000	0.000
72	G	278	ASP	-1	-0.906	-0.976	13.057	-0.211	-0.211	0.000	0.000	0.000	0.000
73	G	279	ILE	0	-0.072	-0.035	12.346	0.043	0.043	0.000	0.000	0.000	0.000
74	G	280	LEU	0	0.005	-0.029	15.726	0.023	0.023	0.000	0.000	0.000	0.000
75	G	281	GLN	0	0.017	0.039	18.648	0.014	0.014	0.000	0.000	0.000	0.000
76	G	282	ALA	0	0.056	0.033	17.808	0.011	0.011	0.000	0.000	0.000	0.000
77	G	283	SER	0	-0.088	-0.063	19.550	0.008	0.008	0.000	0.000	0.000	0.000
78	G	284	ASP	-1	-0.890	-0.952	21.404	-0.009	-0.009	0.000	0.000	0.000	0.000
79	G	285	ASN	0	-0.005	-0.009	22.391	0.003	0.003	0.000	0.000	0.000	0.000
80	G	286	LEU	0	0.016	0.018	21.009	0.004	0.004	0.000	0.000	0.000	0.000
81	G	287	SER	0	-0.014	-0.021	24.894	0.005	0.005	0.000	0.000	0.000	0.000
82	G	288	ARG	1	0.894	0.954	27.397	0.011	0.011	0.000	0.000	0.000	0.000
83	G	289	VAL	0	0.044	0.006	27.050	-0.001	-0.001	0.000	0.000	0.000	0.000
84	G	290	ILE	0	0.010	0.022	27.230	0.001	0.001	0.000	0.000	0.000	0.000
85	G	291	ASN	0	-0.034	-0.044	30.609	0.003	0.003	0.000	0.000	0.000	0.000
86	G	292	SER	0	-0.017	0.008	32.535	-0.002	-0.002	0.000	0.000	0.000	0.000
87	G	293	TYR	0	0.033	0.011	33.201	-0.001	-0.001	0.000	0.000	0.000	0.000
88	G	294	LYS	1	0.907	0.967	32.774	-0.037	-0.037	0.000	0.000	0.000	0.000
89	G	295	THR	0	-0.005	-0.007	36.825	-0.001	-0.001	0.000	0.000	0.000	0.000
90	G	296	ILE	0	0.018	0.006	36.655	0.000	0.000	0.000	0.000	0.000	0.000
91	G	297	ILE	0	-0.047	-0.018	37.692	0.001	0.001	0.000	0.000	0.000	0.000
92	G	298	GLU	-1	-1.009	-1.004	40.351	0.025	0.025	0.000	0.000	0.000	0.000
93	G	299	GLY	0	-0.101	-0.031	42.533	-0.002	-0.002	0.000	0.000	0.000	0.000

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