FMO DATABASE

FMODB ID: R8G98

Calculation Name: 1YN3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YN3

Chain ID: A

ChEMBL ID:

UniProt ID: Q99QS1

Base Structure: X-ray

Registration Date: 2023-09-23

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-702454.373663
FMO2-HF: Nuclear repulsion	665309.393434
FMO2-HF: Total energy	-37144.980229
FMO2-MP2: Total energy	-37256.131341

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(A:157:GLY)

Summations of interaction energy for fragment #1(A:157: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.
-3.102	1.85	4.653	-4.753	-4.852	-0.024

Interaction energy analysis for fragmet #1(A:157:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.029

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	A	159	THR	0	-0.006	0.001	3.785	-1.478	0.480	-0.016	-1.123	-0.820	0.005
4	A	160	VAL	0	-0.017	-0.005	6.317	0.351	0.351	0.000	0.000	0.000	0.000
5	A	161	PRO	0	0.049	0.036	9.247	0.132	0.132	0.000	0.000	0.000	0.000
6	A	162	TYR	0	-0.053	-0.060	11.936	0.061	0.061	0.000	0.000	0.000	0.000
7	A	163	THR	0	0.025	0.009	14.875	0.007	0.007	0.000	0.000	0.000	0.000
8	A	164	ILE	0	0.012	0.011	17.520	0.010	0.010	0.000	0.000	0.000	0.000
9	A	165	THR	0	-0.074	-0.026	20.520	0.004	0.004	0.000	0.000	0.000	0.000
10	A	166	VAL	0	0.028	0.002	24.213	0.007	0.007	0.000	0.000	0.000	0.000
11	A	167	ASN	0	0.008	0.004	26.903	0.007	0.007	0.000	0.000	0.000	0.000
12	A	168	GLY	0	0.012	0.012	29.972	0.005	0.005	0.000	0.000	0.000	0.000
13	A	169	THR	0	-0.034	-0.032	26.604	0.004	0.004	0.000	0.000	0.000	0.000
14	A	170	SER	0	0.007	0.022	28.851	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	171	GLN	0	0.033	0.028	24.907	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	172	ASN	0	0.024	0.011	22.864	0.013	0.013	0.000	0.000	0.000	0.000
17	A	173	ILE	0	-0.025	-0.002	17.546	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	174	LEU	0	0.013	-0.005	16.746	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	175	SER	0	0.009	0.012	13.569	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	176	ASN	0	0.011	-0.009	8.938	-0.118	-0.118	0.000	0.000	0.000	0.000
21	A	177	LEU	0	0.022	0.029	8.619	0.091	0.091	0.000	0.000	0.000	0.000
22	A	178	THR	0	0.015	0.005	2.660	-1.015	-0.603	0.375	-0.271	-0.516	0.000
23	A	179	PHE	0	0.004	0.002	3.650	1.142	1.394	0.000	-0.073	-0.179	0.000
24	A	180	ASN	0	0.037	0.014	2.477	-3.168	-1.630	2.620	-2.247	-1.911	-0.024
25	A	181	LYS	1	0.959	0.980	2.307	-0.738	-0.065	1.657	-1.009	-1.320	-0.005
26	A	182	ASN	0	-0.009	0.003	3.743	0.382	0.501	0.017	-0.030	-0.106	0.000
27	A	183	GLN	0	0.076	0.062	6.950	0.271	0.271	0.000	0.000	0.000	0.000
28	A	184	ASN	0	-0.001	-0.004	8.416	-0.237	-0.237	0.000	0.000	0.000	0.000
29	A	185	ILE	0	-0.008	-0.004	9.879	0.080	0.080	0.000	0.000	0.000	0.000
30	A	186	SER	0	0.015	-0.018	12.765	-0.070	-0.070	0.000	0.000	0.000	0.000
31	A	187	TYR	0	0.022	-0.021	15.430	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	188	LYS	1	0.844	0.926	17.823	-0.049	-0.049	0.000	0.000	0.000	0.000
33	A	189	ASP	-1	-0.800	-0.871	13.094	0.202	0.202	0.000	0.000	0.000	0.000
34	A	190	LEU	0	-0.056	-0.033	12.121	-0.031	-0.031	0.000	0.000	0.000	0.000
35	A	191	GLU	-1	-0.781	-0.867	14.211	-0.051	-0.051	0.000	0.000	0.000	0.000
36	A	192	GLY	0	0.055	0.035	15.742	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	193	LYS	1	0.846	0.921	7.223	0.248	0.248	0.000	0.000	0.000	0.000
38	A	194	VAL	0	0.003	-0.008	13.074	-0.044	-0.044	0.000	0.000	0.000	0.000
39	A	195	LYS	1	0.845	0.901	15.590	0.024	0.024	0.000	0.000	0.000	0.000
40	A	196	SER	0	0.006	0.031	14.306	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	197	VAL	0	-0.009	-0.005	12.869	0.000	0.000	0.000	0.000	0.000	0.000
42	A	198	LEU	0	-0.028	-0.012	15.879	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	199	GLU	-1	-0.883	-0.936	19.386	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	200	SER	0	-0.039	-0.028	16.606	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	201	ASN	0	-0.016	-0.006	15.774	-0.044	-0.044	0.000	0.000	0.000	0.000
46	A	202	ARG	1	0.851	0.894	19.619	0.178	0.178	0.000	0.000	0.000	0.000
47	A	203	GLY	0	0.041	0.053	22.438	0.008	0.008	0.000	0.000	0.000	0.000
48	A	204	ILE	0	-0.066	-0.029	23.169	0.009	0.009	0.000	0.000	0.000	0.000
49	A	205	THR	0	0.045	-0.006	22.919	0.000	0.000	0.000	0.000	0.000	0.000
50	A	206	ASP	-1	-0.820	-0.914	24.060	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	207	VAL	0	0.002	-0.009	25.566	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	208	ASP	-1	-0.789	-0.863	27.025	-0.056	-0.056	0.000	0.000	0.000	0.000
53	A	209	LEU	0	-0.020	-0.014	22.563	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	210	ARG	1	0.868	0.936	27.211	0.009	0.009	0.000	0.000	0.000	0.000
55	A	211	LEU	0	-0.021	-0.001	30.241	0.001	0.001	0.000	0.000	0.000	0.000
56	A	212	SER	0	-0.078	-0.026	29.193	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	213	LYS	1	1.023	0.995	31.315	0.078	0.078	0.000	0.000	0.000	0.000
58	A	214	GLN	0	-0.050	-0.048	28.523	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	215	ALA	0	0.057	0.056	25.147	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	216	LYS	1	0.909	0.955	23.795	0.174	0.174	0.000	0.000	0.000	0.000
61	A	217	TYR	0	0.044	0.013	16.734	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	218	THR	0	-0.040	-0.014	20.018	0.033	0.033	0.000	0.000	0.000	0.000
63	A	219	VAL	0	0.019	0.017	14.924	-0.044	-0.044	0.000	0.000	0.000	0.000
64	A	220	ASN	0	-0.042	-0.030	16.818	0.088	0.088	0.000	0.000	0.000	0.000
65	A	221	PHE	0	0.051	0.013	14.681	-0.082	-0.082	0.000	0.000	0.000	0.000
66	A	222	LYS	1	0.849	0.901	9.821	1.055	1.055	0.000	0.000	0.000	0.000
67	A	223	ASN	0	0.019	0.033	16.371	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	224	GLY	0	0.010	0.012	19.510	0.030	0.030	0.000	0.000	0.000	0.000
69	A	225	THR	0	-0.049	-0.020	20.157	0.020	0.020	0.000	0.000	0.000	0.000
70	A	226	LYS	1	0.995	0.979	20.190	0.175	0.175	0.000	0.000	0.000	0.000
71	A	227	LYS	1	0.949	0.991	20.030	0.138	0.138	0.000	0.000	0.000	0.000
72	A	228	VAL	0	-0.014	-0.004	20.997	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	229	ILE	0	-0.042	-0.020	19.931	0.022	0.022	0.000	0.000	0.000	0.000
74	A	230	ASP	-1	-0.844	-0.919	23.036	-0.088	-0.088	0.000	0.000	0.000	0.000
75	A	231	LEU	0	-0.026	-0.046	20.036	0.008	0.008	0.000	0.000	0.000	0.000
76	A	232	LYS	1	0.810	0.904	23.988	0.073	0.073	0.000	0.000	0.000	0.000
77	A	233	SER	0	-0.040	-0.007	26.333	0.015	0.015	0.000	0.000	0.000	0.000
78	A	234	GLY	0	0.045	0.027	25.477	0.000	0.000	0.000	0.000	0.000	0.000
79	A	235	ILE	0	-0.055	-0.024	26.967	0.011	0.011	0.000	0.000	0.000	0.000
80	A	236	TYR	0	0.003	-0.020	22.041	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	237	THR	0	-0.056	-0.059	21.941	0.001	0.001	0.000	0.000	0.000	0.000
82	A	238	ALA	0	0.137	0.120	21.490	0.003	0.003	0.000	0.000	0.000	0.000
83	A	239	ASN	0	-0.049	-0.081	18.982	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	240	LEU	0	-0.116	-0.010	15.651	0.002	0.002	0.000	0.000	0.000	0.000
85	A	241	ILE	0	0.105	0.042	13.248	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	242	ASN	0	0.065	0.026	9.913	-0.051	-0.051	0.000	0.000	0.000	0.000
87	A	243	SER	0	0.012	-0.016	5.801	-0.102	-0.102	0.000	0.000	0.000	0.000
88	A	244	SER	0	0.001	-0.003	7.612	-0.414	-0.414	0.000	0.000	0.000	0.000
89	A	245	ASP	-1	-0.856	-0.918	8.715	-0.384	-0.384	0.000	0.000	0.000	0.000
90	A	246	ILE	0	-0.058	-0.024	10.302	0.059	0.059	0.000	0.000	0.000	0.000
91	A	247	LYS	1	0.919	0.956	11.268	0.270	0.270	0.000	0.000	0.000	0.000
92	A	248	SER	0	-0.004	-0.009	13.373	-0.079	-0.079	0.000	0.000	0.000	0.000
93	A	249	ILE	0	0.001	0.007	12.408	0.070	0.070	0.000	0.000	0.000	0.000
94	A	250	ASN	0	-0.041	-0.007	15.828	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	251	ILE	0	0.059	0.025	16.000	0.031	0.031	0.000	0.000	0.000	0.000
96	A	252	ASN	0	-0.034	-0.021	20.252	0.002	0.002	0.000	0.000	0.000	0.000
97	A	253	ILE	0	0.065	0.045	23.022	0.012	0.012	0.000	0.000	0.000	0.000
98	A	254	ASP	-1	-0.847	-0.909	26.327	-0.087	-0.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:157:GLY)