FMO DATABASE

FMODB ID: YY8V2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-777013.664079
FMO2-HF: Nuclear repulsion	736504.448535
FMO2-HF: Total energy	-40509.215544
FMO2-MP2: Total energy	-40628.559114

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.
-14.883	-6.853	4.988	-6.282	-6.737	-0.029

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 : 0.064 / q_NPA : 0.027

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	A	44	GLU	-1	-0.812	-0.888	3.481	-3.007	-0.383	-0.019	-1.399	-1.206	0.003
4	A	45	MET	0	-0.012	0.007	4.748	-1.516	-1.503	-0.001	-0.007	-0.005	0.000
5	A	46	GLN	0	-0.034	-0.037	7.558	0.113	0.113	0.000	0.000	0.000	0.000
6	A	47	ASN	0	0.011	0.009	9.620	-0.080	-0.080	0.000	0.000	0.000	0.000
7	A	48	VAL	0	0.015	0.011	12.212	0.014	0.014	0.000	0.000	0.000	0.000
8	A	49	PRO	0	0.017	0.017	14.658	0.030	0.030	0.000	0.000	0.000	0.000
9	A	50	TYR	0	-0.085	-0.071	18.481	-0.036	-0.036	0.000	0.000	0.000	0.000
10	A	51	THR	0	0.006	-0.016	20.696	0.029	0.029	0.000	0.000	0.000	0.000
11	A	52	ILE	0	0.024	0.016	23.568	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	53	ALA	0	-0.016	-0.002	26.488	0.014	0.014	0.000	0.000	0.000	0.000
13	A	54	VAL	0	0.017	-0.003	30.000	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	55	ASP	-1	-0.836	-0.905	32.484	-0.090	-0.090	0.000	0.000	0.000	0.000
15	A	56	GLY	0	-0.003	0.011	34.325	0.006	0.006	0.000	0.000	0.000	0.000
16	A	57	ILE	0	0.000	0.007	33.649	0.000	0.000	0.000	0.000	0.000	0.000
17	A	58	MET	0	-0.001	-0.003	28.604	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	59	ALA	0	0.021	0.017	27.594	0.007	0.007	0.000	0.000	0.000	0.000
19	A	60	PHE	0	-0.001	-0.001	29.604	0.002	0.002	0.000	0.000	0.000	0.000
20	A	61	ASN	0	-0.010	-0.014	27.356	0.002	0.002	0.000	0.000	0.000	0.000
21	A	62	GLN	0	-0.022	-0.004	21.753	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	63	SER	0	0.012	0.017	22.020	0.013	0.013	0.000	0.000	0.000	0.000
23	A	64	TYR	0	0.015	-0.007	16.644	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	65	LEU	0	0.001	0.014	13.280	0.011	0.011	0.000	0.000	0.000	0.000
25	A	66	ASN	0	-0.017	-0.018	11.611	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	67	LEU	0	-0.005	-0.012	8.466	0.035	0.035	0.000	0.000	0.000	0.000
27	A	68	PRO	0	0.009	0.000	4.080	0.296	0.440	0.000	-0.045	-0.100	0.000
28	A	69	LYS	1	0.858	0.938	3.080	-0.627	-0.099	0.021	-0.122	-0.427	-0.001
29	A	70	ASP	-1	-0.871	-0.929	2.258	-8.697	-6.401	3.224	-2.674	-2.846	-0.019
30	A	71	SER	0	-0.008	-0.011	2.157	-2.722	-0.361	1.763	-2.001	-2.123	-0.012
31	A	72	GLN	0	-0.023	0.002	4.232	0.392	0.456	0.000	-0.034	-0.030	0.000
32	A	73	LEU	0	0.022	0.014	6.641	0.069	0.069	0.000	0.000	0.000	0.000
33	A	74	SER	0	0.076	0.040	9.717	0.123	0.123	0.000	0.000	0.000	0.000
34	A	75	TYR	0	-0.004	-0.015	13.498	0.010	0.010	0.000	0.000	0.000	0.000
35	A	76	LEU	0	-0.026	0.006	16.328	0.036	0.036	0.000	0.000	0.000	0.000
36	A	77	ASP	-1	-0.843	-0.925	12.740	-0.549	-0.549	0.000	0.000	0.000	0.000
37	A	78	LEU	0	-0.042	-0.018	13.346	0.025	0.025	0.000	0.000	0.000	0.000
38	A	79	GLY	0	0.041	0.015	15.475	0.043	0.043	0.000	0.000	0.000	0.000
39	A	80	ASN	0	-0.033	-0.022	17.741	0.059	0.059	0.000	0.000	0.000	0.000
40	A	81	LYS	1	0.914	0.959	11.494	0.686	0.686	0.000	0.000	0.000	0.000
41	A	82	VAL	0	0.012	0.011	17.972	0.032	0.032	0.000	0.000	0.000	0.000
42	A	83	LYS	1	0.793	0.874	20.633	0.259	0.259	0.000	0.000	0.000	0.000
43	A	84	ALA	0	0.006	0.014	20.499	0.021	0.021	0.000	0.000	0.000	0.000
44	A	85	LEU	0	0.034	0.016	18.902	0.017	0.017	0.000	0.000	0.000	0.000
45	A	86	LEU	0	-0.025	-0.017	22.904	0.020	0.020	0.000	0.000	0.000	0.000
46	A	87	TYR	0	-0.053	-0.020	25.849	0.018	0.018	0.000	0.000	0.000	0.000
47	A	88	ASP	-1	-0.882	-0.950	23.567	-0.133	-0.133	0.000	0.000	0.000	0.000
48	A	89	GLU	-1	-0.811	-0.885	24.783	-0.137	-0.137	0.000	0.000	0.000	0.000
49	A	90	ARG	1	0.726	0.848	27.858	0.134	0.134	0.000	0.000	0.000	0.000
50	A	91	GLY	0	0.037	0.038	30.280	0.006	0.006	0.000	0.000	0.000	0.000
51	A	92	VAL	0	-0.086	-0.050	29.135	0.005	0.005	0.000	0.000	0.000	0.000
52	A	93	THR	0	0.053	0.034	29.174	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	94	PRO	0	0.058	0.002	28.427	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	95	GLU	-1	-0.810	-0.874	30.645	-0.091	-0.091	0.000	0.000	0.000	0.000
55	A	96	LYS	1	0.931	0.962	32.597	0.097	0.097	0.000	0.000	0.000	0.000
56	A	97	ILE	0	0.018	0.004	27.293	0.001	0.001	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.862	0.906	31.614	0.103	0.103	0.000	0.000	0.000	0.000
58	A	99	ASN	0	-0.042	-0.031	34.020	0.004	0.004	0.000	0.000	0.000	0.000
59	A	100	ALA	0	-0.034	0.019	33.521	0.005	0.005	0.000	0.000	0.000	0.000
60	A	101	LYS	1	0.941	0.979	35.675	0.091	0.091	0.000	0.000	0.000	0.000
61	A	102	SER	0	-0.037	-0.033	32.446	0.000	0.000	0.000	0.000	0.000	0.000
62	A	103	ALA	0	0.017	0.011	29.287	0.004	0.004	0.000	0.000	0.000	0.000
63	A	104	VAL	0	0.003	0.009	26.367	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	105	TYR	0	0.054	0.021	18.474	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	106	THR	0	-0.005	-0.012	23.043	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	107	ILE	0	0.001	0.010	16.567	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	108	THR	0	0.006	0.010	19.395	0.035	0.035	0.000	0.000	0.000	0.000
68	A	109	TRP	0	0.039	0.007	13.831	-0.061	-0.061	0.000	0.000	0.000	0.000
69	A	110	LYS	1	0.834	0.886	11.669	0.663	0.663	0.000	0.000	0.000	0.000
70	A	111	ASP	-1	-0.788	-0.874	16.980	-0.259	-0.259	0.000	0.000	0.000	0.000
71	A	112	GLY	0	-0.007	0.009	20.205	0.032	0.032	0.000	0.000	0.000	0.000
72	A	113	SER	0	-0.036	-0.025	20.801	0.013	0.013	0.000	0.000	0.000	0.000
73	A	114	LYS	1	0.869	0.889	21.773	0.214	0.214	0.000	0.000	0.000	0.000
74	A	115	LYS	1	0.898	0.966	18.904	0.361	0.361	0.000	0.000	0.000	0.000
75	A	116	GLU	-1	-0.871	-0.907	21.827	-0.199	-0.199	0.000	0.000	0.000	0.000
76	A	117	VAL	0	-0.054	-0.033	20.234	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	118	ASP	-1	-0.818	-0.906	23.721	-0.156	-0.156	0.000	0.000	0.000	0.000
78	A	119	LEU	0	0.020	0.001	23.227	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	120	LYS	1	0.770	0.877	26.656	0.123	0.123	0.000	0.000	0.000	0.000
80	A	121	LYS	1	0.853	0.917	27.925	0.162	0.162	0.000	0.000	0.000	0.000
81	A	122	ASP	-1	-0.829	-0.878	24.067	-0.228	-0.228	0.000	0.000	0.000	0.000
82	A	123	SER	0	-0.030	-0.022	24.565	0.014	0.014	0.000	0.000	0.000	0.000
83	A	124	TYR	0	0.030	0.009	18.920	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	125	THR	0	0.007	-0.002	18.882	0.001	0.001	0.000	0.000	0.000	0.000
85	A	126	ALA	0	0.041	0.021	17.993	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	127	ASN	0	-0.058	-0.024	16.680	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	128	LEU	0	0.026	0.008	11.089	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	129	PHE	0	-0.058	-0.033	10.796	0.079	0.079	0.000	0.000	0.000	0.000
89	A	130	ASP	-1	-0.730	-0.843	8.653	-1.434	-1.434	0.000	0.000	0.000	0.000
90	A	131	SER	0	-0.007	-0.028	6.403	0.252	0.252	0.000	0.000	0.000	0.000
91	A	132	ASN	0	-0.018	-0.021	6.371	-0.097	-0.097	0.000	0.000	0.000	0.000
92	A	133	SER	0	-0.015	-0.020	9.193	0.266	0.266	0.000	0.000	0.000	0.000
93	A	134	ILE	0	-0.026	0.005	11.874	0.132	0.132	0.000	0.000	0.000	0.000
94	A	135	LYS	1	0.820	0.919	13.528	0.252	0.252	0.000	0.000	0.000	0.000
95	A	136	GLN	0	-0.029	-0.027	16.175	0.027	0.027	0.000	0.000	0.000	0.000
96	A	137	ILE	0	-0.031	-0.008	15.241	-0.024	-0.024	0.000	0.000	0.000	0.000
97	A	138	ASP	-1	-0.801	-0.862	19.680	-0.201	-0.201	0.000	0.000	0.000	0.000
98	A	139	ILE	0	0.005	-0.001	20.935	0.000	0.000	0.000	0.000	0.000	0.000
99	A	140	ASN	0	-0.034	-0.028	24.690	0.023	0.023	0.000	0.000	0.000	0.000
100	A	141	VAL	0	0.035	0.017	28.413	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	142	LYS	1	0.920	0.972	31.054	0.135	0.135	0.000	0.000	0.000	0.000
102	A	143	THR	0	0.043	-0.007	34.770	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	144	LYS	1	0.928	0.970	36.820	0.093	0.093	0.000	0.000	0.000	0.000

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