FMO DATABASE

FMODB ID: KR143

Calculation Name: 1YN5-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YN5

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-775806.519975
FMO2-HF: Nuclear repulsion	735299.248419
FMO2-HF: Total energy	-40507.271556
FMO2-MP2: Total energy	-40626.700623

3D Structure Molmil

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:42:ALA )

Summations of interaction energy for fragment #1(A:42:ALA )

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.
-14.775	-6.85	0.833	-4.081	-4.677	-0.018

Interaction energy analysis for fragmet #1(A:42:ALA )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / 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	A	44	GLU	-1	-0.878	-0.930	3.766	-4.026	-0.635	-0.030	-1.763	-1.598	-0.001
4	A	45	MET	0	-0.017	-0.002	5.669	-1.202	-1.202	0.000	0.000	0.000	0.000
5	A	46	GLN	0	0.042	0.026	8.403	0.105	0.105	0.000	0.000	0.000	0.000
6	A	47	ASN	0	0.000	-0.004	10.490	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	48	VAL	0	-0.041	-0.025	12.595	-0.015	-0.015	0.000	0.000	0.000	0.000
8	A	49	PRO	0	0.000	0.004	15.316	0.031	0.031	0.000	0.000	0.000	0.000
9	A	50	TYR	0	-0.038	-0.078	18.969	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	51	THR	0	-0.004	-0.004	21.143	0.029	0.029	0.000	0.000	0.000	0.000
11	A	52	ILE	0	0.031	0.009	24.489	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	53	ALA	0	-0.010	-0.020	26.986	0.014	0.014	0.000	0.000	0.000	0.000
13	A	54	VAL	0	0.007	-0.001	30.387	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	55	ASP	-1	-0.812	-0.920	32.706	-0.090	-0.090	0.000	0.000	0.000	0.000
15	A	56	GLY	0	-0.055	-0.022	34.481	0.006	0.006	0.000	0.000	0.000	0.000
16	A	57	ILE	0	0.005	0.011	34.013	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	58	MET	0	0.023	0.006	28.383	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	59	ALA	0	-0.014	-0.009	27.961	0.009	0.009	0.000	0.000	0.000	0.000
19	A	60	PHE	0	0.027	0.036	29.976	0.000	0.000	0.000	0.000	0.000	0.000
20	A	61	ASN	0	-0.048	-0.033	27.939	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	62	GLN	0	0.005	-0.020	23.193	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	63	SER	0	0.028	0.037	21.936	0.015	0.015	0.000	0.000	0.000	0.000
23	A	64	TYR	0	-0.022	-0.023	17.188	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	65	LEU	0	0.027	0.024	13.649	0.022	0.022	0.000	0.000	0.000	0.000
25	A	66	ASN	0	0.044	0.017	11.563	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	67	LEU	0	-0.069	-0.043	9.125	0.022	0.022	0.000	0.000	0.000	0.000
27	A	68	PRO	0	-0.015	-0.007	4.303	0.177	0.315	0.000	-0.056	-0.083	0.000
28	A	69	LYS	1	0.920	0.980	3.457	0.188	0.566	0.005	-0.062	-0.320	0.000
29	A	70	ASP	-1	-0.911	-0.962	2.434	-8.098	-6.190	0.692	-1.155	-1.445	-0.008
30	A	71	SER	0	-0.026	-0.020	3.011	-3.318	-1.209	0.166	-1.035	-1.240	-0.009
31	A	72	GLN	0	0.045	0.059	4.643	0.622	0.623	0.000	-0.010	0.009	0.000
32	A	73	LEU	0	0.003	0.007	6.608	0.173	0.173	0.000	0.000	0.000	0.000
33	A	74	SER	0	0.086	0.063	9.830	0.127	0.127	0.000	0.000	0.000	0.000
34	A	75	TYR	0	0.008	-0.015	13.468	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	76	LEU	0	-0.027	0.010	16.377	0.035	0.035	0.000	0.000	0.000	0.000
36	A	77	ASP	-1	-0.862	-0.930	12.708	-0.431	-0.431	0.000	0.000	0.000	0.000
37	A	78	LEU	0	-0.063	-0.026	14.299	0.022	0.022	0.000	0.000	0.000	0.000
38	A	79	GLY	0	0.023	-0.002	15.790	0.039	0.039	0.000	0.000	0.000	0.000
39	A	80	ASN	0	-0.008	-0.004	17.641	0.055	0.055	0.000	0.000	0.000	0.000
40	A	81	LYS	1	0.971	0.982	12.204	0.578	0.578	0.000	0.000	0.000	0.000
41	A	82	VAL	0	-0.003	0.009	18.351	0.030	0.030	0.000	0.000	0.000	0.000
42	A	83	LYS	1	0.842	0.900	20.903	0.235	0.235	0.000	0.000	0.000	0.000
43	A	84	ALA	0	-0.012	0.001	20.602	0.020	0.020	0.000	0.000	0.000	0.000
44	A	85	LEU	0	0.021	0.019	19.599	0.015	0.015	0.000	0.000	0.000	0.000
45	A	86	LEU	0	-0.025	-0.006	23.255	0.019	0.019	0.000	0.000	0.000	0.000
46	A	87	TYR	0	-0.041	-0.008	26.152	0.016	0.016	0.000	0.000	0.000	0.000
47	A	88	ASP	-1	-0.904	-0.960	24.191	-0.111	-0.111	0.000	0.000	0.000	0.000
48	A	89	GLU	-1	-0.864	-0.906	24.270	-0.143	-0.143	0.000	0.000	0.000	0.000
49	A	90	ARG	1	0.790	0.895	27.954	0.128	0.128	0.000	0.000	0.000	0.000
50	A	91	GLY	0	0.020	0.036	30.125	0.006	0.006	0.000	0.000	0.000	0.000
51	A	92	VAL	0	-0.070	-0.032	29.518	0.005	0.005	0.000	0.000	0.000	0.000
52	A	93	THR	0	0.074	0.027	29.638	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	94	PRO	0	0.034	-0.011	28.456	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	95	GLU	-1	-0.940	-0.978	30.634	-0.078	-0.078	0.000	0.000	0.000	0.000
55	A	96	LYS	1	0.942	0.991	33.035	0.091	0.091	0.000	0.000	0.000	0.000
56	A	97	ILE	0	0.022	0.008	27.610	0.000	0.000	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.910	0.944	31.922	0.097	0.097	0.000	0.000	0.000	0.000
58	A	99	ASN	0	-0.007	-0.006	34.072	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	100	ALA	0	-0.019	0.028	33.558	0.003	0.003	0.000	0.000	0.000	0.000
60	A	101	LYS	1	0.956	1.003	35.634	0.093	0.093	0.000	0.000	0.000	0.000
61	A	102	SER	0	-0.062	-0.058	32.692	0.001	0.001	0.000	0.000	0.000	0.000
62	A	103	ALA	0	0.020	0.017	29.163	0.003	0.003	0.000	0.000	0.000	0.000
63	A	104	VAL	0	0.018	0.038	26.479	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	105	TYR	0	0.045	0.018	19.100	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	106	THR	0	-0.006	-0.005	23.370	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	107	ILE	0	-0.006	0.002	16.939	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	108	THR	0	-0.021	-0.011	19.647	0.033	0.033	0.000	0.000	0.000	0.000
68	A	109	TRP	0	0.033	0.002	14.167	-0.067	-0.067	0.000	0.000	0.000	0.000
69	A	110	LYS	1	0.847	0.908	12.691	0.738	0.738	0.000	0.000	0.000	0.000
70	A	111	ASP	-1	-0.837	-0.864	17.892	-0.319	-0.319	0.000	0.000	0.000	0.000
71	A	112	GLY	0	-0.024	-0.007	20.700	0.036	0.036	0.000	0.000	0.000	0.000
72	A	113	SER	0	-0.054	-0.064	21.327	0.019	0.019	0.000	0.000	0.000	0.000
73	A	114	LYS	1	0.920	0.938	21.926	0.222	0.222	0.000	0.000	0.000	0.000
74	A	115	LYS	1	0.937	0.987	19.682	0.368	0.368	0.000	0.000	0.000	0.000
75	A	116	GLU	-1	-0.922	-0.952	22.585	-0.202	-0.202	0.000	0.000	0.000	0.000
76	A	117	VAL	0	-0.044	-0.027	20.706	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	118	ASP	-1	-0.820	-0.930	24.015	-0.159	-0.159	0.000	0.000	0.000	0.000
78	A	119	LEU	0	-0.015	-0.025	23.185	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	120	LYS	1	0.793	0.905	26.733	0.127	0.127	0.000	0.000	0.000	0.000
80	A	121	LYS	1	0.894	0.951	28.429	0.158	0.158	0.000	0.000	0.000	0.000
81	A	122	ASP	-1	-0.785	-0.854	24.221	-0.217	-0.217	0.000	0.000	0.000	0.000
82	A	123	SER	0	-0.031	-0.048	24.779	0.014	0.014	0.000	0.000	0.000	0.000
83	A	124	TYR	0	-0.028	-0.007	18.889	-0.018	-0.018	0.000	0.000	0.000	0.000
84	A	125	THR	0	0.008	-0.001	18.953	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	126	ALA	0	0.047	0.015	17.904	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	127	ASN	0	-0.040	-0.008	16.506	-0.038	-0.038	0.000	0.000	0.000	0.000
87	A	128	LEU	0	0.032	-0.006	11.379	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	129	PHE	0	-0.051	-0.032	11.347	0.061	0.061	0.000	0.000	0.000	0.000
89	A	130	ASP	-1	-0.856	-0.930	8.999	-1.542	-1.542	0.000	0.000	0.000	0.000
90	A	131	SER	0	-0.023	-0.054	6.732	0.074	0.074	0.000	0.000	0.000	0.000
91	A	132	ASN	0	0.000	0.006	6.796	0.038	0.038	0.000	0.000	0.000	0.000
92	A	133	SER	0	0.020	0.000	9.773	0.255	0.255	0.000	0.000	0.000	0.000
93	A	134	ILE	0	-0.001	0.014	12.184	0.149	0.149	0.000	0.000	0.000	0.000
94	A	135	LYS	1	0.902	0.963	13.975	0.281	0.281	0.000	0.000	0.000	0.000
95	A	136	GLN	0	-0.063	-0.050	16.824	0.017	0.017	0.000	0.000	0.000	0.000
96	A	137	ILE	0	-0.028	-0.003	15.872	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	138	ASP	-1	-0.817	-0.860	20.056	-0.214	-0.214	0.000	0.000	0.000	0.000
98	A	139	ILE	0	-0.006	-0.015	21.560	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	140	ASN	0	-0.052	-0.029	25.142	0.023	0.023	0.000	0.000	0.000	0.000
100	A	141	VAL	0	0.038	0.018	28.784	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	142	LYS	1	0.907	0.957	31.224	0.131	0.131	0.000	0.000	0.000	0.000
102	A	143	THR	0	0.003	-0.022	34.950	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	144	LYS	0	0.048	0.033	37.111	0.017	0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:42:ALA )