FMO DATABASE

FMODB ID: 43ZLN

Calculation Name: 1YN5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YN5

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-06-20

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-775990.799162
FMO2-HF: Nuclear repulsion	735483.061233
FMO2-HF: Total energy	-40507.73793
FMO2-MP2: Total energy	-40627.161968

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: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.
-14.518	-6.583	0.815	-4.048	-4.7	-0.017

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 : 0.026 / 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	-0.929	3.766	-4.037	-0.601	-0.047	-1.770	-1.619	-0.001
4	A	45	MET	0	-0.019	-0.004	5.666	-1.183	-1.183	0.000	0.000	0.000	0.000
5	A	46	GLN	0	0.044	0.028	8.400	0.105	0.105	0.000	0.000	0.000	0.000
6	A	47	ASN	0	-0.002	-0.004	10.489	-0.014	-0.014	0.000	0.000	0.000	0.000
7	A	48	VAL	0	-0.041	-0.025	12.595	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	49	PRO	0	0.003	0.004	15.316	0.029	0.029	0.000	0.000	0.000	0.000
9	A	50	TYR	0	-0.040	-0.079	18.969	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	51	THR	0	0.000	-0.002	21.143	0.028	0.028	0.000	0.000	0.000	0.000
11	A	52	ILE	0	0.033	0.010	24.489	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	53	ALA	0	-0.010	-0.019	26.986	0.014	0.014	0.000	0.000	0.000	0.000
13	A	54	VAL	0	0.007	-0.002	30.387	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	55	ASP	-1	-0.822	-0.927	32.706	-0.090	-0.090	0.000	0.000	0.000	0.000
15	A	56	GLY	0	-0.047	-0.019	34.480	0.006	0.006	0.000	0.000	0.000	0.000
16	A	57	ILE	0	0.009	0.014	34.009	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	58	MET	0	0.024	0.007	28.383	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	59	ALA	0	-0.013	-0.008	27.961	0.009	0.009	0.000	0.000	0.000	0.000
19	A	60	PHE	0	0.029	0.037	29.976	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	61	ASN	0	-0.043	-0.032	27.939	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	62	GLN	0	0.007	-0.020	23.192	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	63	SER	0	0.024	0.037	21.935	0.015	0.015	0.000	0.000	0.000	0.000
23	A	64	TYR	0	-0.021	-0.022	17.188	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	65	LEU	0	0.024	0.023	13.649	0.023	0.023	0.000	0.000	0.000	0.000
25	A	66	ASN	0	0.045	0.017	11.564	-0.074	-0.074	0.000	0.000	0.000	0.000
26	A	67	LEU	0	-0.072	-0.043	9.125	0.034	0.034	0.000	0.000	0.000	0.000
27	A	68	PRO	0	-0.011	-0.004	4.303	0.202	0.342	-0.001	-0.055	-0.083	0.000
28	A	69	LYS	1	0.917	0.979	3.456	0.229	0.611	0.004	-0.062	-0.324	0.000
29	A	70	ASP	-1	-0.908	-0.961	2.438	-8.000	-6.117	0.693	-1.133	-1.443	-0.007
30	A	71	SER	0	-0.024	-0.018	3.013	-3.287	-1.194	0.167	-1.019	-1.240	-0.009
31	A	72	GLN	0	0.043	0.058	4.643	0.578	0.579	-0.001	-0.009	0.009	0.000
32	A	73	LEU	0	0.007	0.008	6.608	0.170	0.170	0.000	0.000	0.000	0.000
33	A	74	SER	0	0.086	0.064	9.830	0.120	0.120	0.000	0.000	0.000	0.000
34	A	75	TYR	0	0.007	-0.016	13.468	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	76	LEU	0	-0.030	0.009	16.377	0.033	0.033	0.000	0.000	0.000	0.000
36	A	77	ASP	-1	-0.861	-0.929	12.706	-0.429	-0.429	0.000	0.000	0.000	0.000
37	A	78	LEU	0	-0.060	-0.025	14.299	0.023	0.023	0.000	0.000	0.000	0.000
38	A	79	GLY	0	0.019	-0.004	15.790	0.037	0.037	0.000	0.000	0.000	0.000
39	A	80	ASN	0	-0.008	-0.004	17.640	0.055	0.055	0.000	0.000	0.000	0.000
40	A	81	LYS	1	0.972	0.983	12.203	0.584	0.584	0.000	0.000	0.000	0.000
41	A	82	VAL	0	0.001	0.010	18.351	0.030	0.030	0.000	0.000	0.000	0.000
42	A	83	LYS	1	0.835	0.897	20.903	0.234	0.234	0.000	0.000	0.000	0.000
43	A	84	ALA	0	-0.010	0.003	20.602	0.020	0.020	0.000	0.000	0.000	0.000
44	A	85	LEU	0	0.024	0.021	19.599	0.015	0.015	0.000	0.000	0.000	0.000
45	A	86	LEU	0	-0.031	-0.009	23.255	0.019	0.019	0.000	0.000	0.000	0.000
46	A	87	TYR	0	-0.039	-0.009	26.152	0.016	0.016	0.000	0.000	0.000	0.000
47	A	88	ASP	-1	-0.902	-0.959	24.192	-0.113	-0.113	0.000	0.000	0.000	0.000
48	A	89	GLU	-1	-0.861	-0.904	24.270	-0.146	-0.146	0.000	0.000	0.000	0.000
49	A	90	ARG	1	0.791	0.895	27.954	0.129	0.129	0.000	0.000	0.000	0.000
50	A	91	GLY	0	0.021	0.036	30.125	0.006	0.006	0.000	0.000	0.000	0.000
51	A	92	VAL	0	-0.077	-0.036	29.518	0.005	0.005	0.000	0.000	0.000	0.000
52	A	93	THR	0	0.078	0.031	29.637	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	94	PRO	0	0.042	-0.007	28.455	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	95	GLU	-1	-0.935	-0.976	30.633	-0.078	-0.078	0.000	0.000	0.000	0.000
55	A	96	LYS	1	0.940	0.988	33.035	0.092	0.092	0.000	0.000	0.000	0.000
56	A	97	ILE	0	0.025	0.008	27.610	0.000	0.000	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.919	0.950	31.922	0.097	0.097	0.000	0.000	0.000	0.000
58	A	99	ASN	0	-0.004	-0.002	34.072	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	100	ALA	0	-0.034	0.019	33.558	0.003	0.003	0.000	0.000	0.000	0.000
60	A	101	LYS	1	0.933	0.983	35.634	0.094	0.094	0.000	0.000	0.000	0.000
61	A	102	SER	0	-0.043	-0.049	32.693	0.002	0.002	0.000	0.000	0.000	0.000
62	A	103	ALA	0	0.020	0.017	29.163	0.004	0.004	0.000	0.000	0.000	0.000
63	A	104	VAL	0	0.024	0.041	26.480	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	105	TYR	0	0.048	0.020	19.100	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	106	THR	0	-0.013	-0.007	23.370	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	107	ILE	0	0.005	0.006	16.939	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	108	THR	0	-0.026	-0.013	19.648	0.033	0.033	0.000	0.000	0.000	0.000
68	A	109	TRP	0	0.034	0.002	14.167	-0.064	-0.064	0.000	0.000	0.000	0.000
69	A	110	LYS	1	0.851	0.909	12.692	0.739	0.739	0.000	0.000	0.000	0.000
70	A	111	ASP	-1	-0.835	-0.863	17.894	-0.321	-0.321	0.000	0.000	0.000	0.000
71	A	112	GLY	0	-0.023	-0.007	20.702	0.035	0.035	0.000	0.000	0.000	0.000
72	A	113	SER	0	-0.053	-0.063	21.327	0.019	0.019	0.000	0.000	0.000	0.000
73	A	114	LYS	1	0.917	0.937	21.926	0.223	0.223	0.000	0.000	0.000	0.000
74	A	115	LYS	1	0.940	0.989	19.682	0.368	0.368	0.000	0.000	0.000	0.000
75	A	116	GLU	-1	-0.923	-0.954	22.585	-0.203	-0.203	0.000	0.000	0.000	0.000
76	A	117	VAL	0	-0.043	-0.025	20.706	0.000	0.000	0.000	0.000	0.000	0.000
77	A	118	ASP	-1	-0.820	-0.930	24.015	-0.160	-0.160	0.000	0.000	0.000	0.000
78	A	119	LEU	0	-0.011	-0.023	23.185	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	120	LYS	1	0.786	0.901	26.733	0.127	0.127	0.000	0.000	0.000	0.000
80	A	121	LYS	1	0.897	0.953	28.430	0.159	0.159	0.000	0.000	0.000	0.000
81	A	122	ASP	-1	-0.785	-0.855	24.219	-0.217	-0.217	0.000	0.000	0.000	0.000
82	A	123	SER	0	-0.030	-0.047	24.775	0.014	0.014	0.000	0.000	0.000	0.000
83	A	124	TYR	0	-0.022	-0.005	18.886	-0.018	-0.018	0.000	0.000	0.000	0.000
84	A	125	THR	0	0.005	-0.002	18.953	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	126	ALA	0	0.049	0.016	17.902	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	127	ASN	0	-0.039	-0.008	16.503	-0.035	-0.035	0.000	0.000	0.000	0.000
87	A	128	LEU	0	0.031	-0.005	11.375	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	129	PHE	0	-0.052	-0.033	11.347	0.063	0.063	0.000	0.000	0.000	0.000
89	A	130	ASP	-1	-0.853	-0.928	8.999	-1.530	-1.530	0.000	0.000	0.000	0.000
90	A	131	SER	0	-0.025	-0.055	6.732	0.076	0.076	0.000	0.000	0.000	0.000
91	A	132	ASN	0	0.003	0.007	6.803	0.031	0.031	0.000	0.000	0.000	0.000
92	A	133	SER	0	0.020	0.000	9.773	0.246	0.246	0.000	0.000	0.000	0.000
93	A	134	ILE	0	-0.005	0.012	12.184	0.148	0.148	0.000	0.000	0.000	0.000
94	A	135	LYS	1	0.905	0.963	13.975	0.279	0.279	0.000	0.000	0.000	0.000
95	A	136	GLN	0	-0.061	-0.049	16.824	0.015	0.015	0.000	0.000	0.000	0.000
96	A	137	ILE	0	-0.031	-0.003	15.872	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	138	ASP	-1	-0.815	-0.859	20.056	-0.217	-0.217	0.000	0.000	0.000	0.000
98	A	139	ILE	0	-0.004	-0.014	21.560	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	140	ASN	0	-0.048	-0.027	25.142	0.023	0.023	0.000	0.000	0.000	0.000
100	A	141	VAL	0	0.044	0.023	28.784	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	142	LYS	1	0.919	0.966	31.224	0.132	0.132	0.000	0.000	0.000	0.000
102	A	143	THR	0	0.031	-0.001	34.950	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	144	LYS	1	0.947	0.979	37.111	0.102	0.102	0.000	0.000	0.000	0.000

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