FMO DATABASE

FMODB ID: 536NZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-776032.150179
FMO2-HF: Nuclear repulsion	735523.455223
FMO2-HF: Total energy	-40508.694956
FMO2-MP2: Total energy	-40628.044406

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.
-13.311	-5.477	0.892	-4.072	-4.655	-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 : 0.029 / q_NPA : 0.006

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	-0.835	-0.906	3.766	-4.012	-0.731	-0.051	-1.671	-1.560	0.000
4	A	45	MET	0	0.000	0.017	5.619	-1.155	-1.155	0.000	0.000	0.000	0.000
5	A	46	GLN	0	-0.015	-0.011	8.352	0.134	0.134	0.000	0.000	0.000	0.000
6	A	47	ASN	0	0.008	0.002	10.458	0.001	0.001	0.000	0.000	0.000	0.000
7	A	48	VAL	0	-0.009	-0.009	12.546	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	49	PRO	0	0.021	0.012	15.295	0.029	0.029	0.000	0.000	0.000	0.000
9	A	50	TYR	0	-0.042	-0.057	19.014	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	51	THR	0	-0.006	-0.014	21.130	0.029	0.029	0.000	0.000	0.000	0.000
11	A	52	ILE	0	0.014	0.007	24.064	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	53	ALA	0	0.005	-0.005	26.982	0.014	0.014	0.000	0.000	0.000	0.000
13	A	54	VAL	0	0.015	-0.001	30.384	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	55	ASP	-1	-0.833	-0.911	32.707	-0.091	-0.091	0.000	0.000	0.000	0.000
15	A	56	GLY	0	-0.028	-0.009	34.484	0.006	0.006	0.000	0.000	0.000	0.000
16	A	57	ILE	0	0.005	0.014	33.991	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	58	MET	0	-0.009	-0.005	28.747	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	59	ALA	0	0.003	0.006	27.958	0.008	0.008	0.000	0.000	0.000	0.000
19	A	60	PHE	0	0.036	0.039	29.966	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	61	ASN	0	-0.086	-0.054	28.253	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	62	GLN	0	0.050	0.021	22.939	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	63	SER	0	-0.001	0.004	21.970	0.014	0.014	0.000	0.000	0.000	0.000
23	A	64	TYR	0	-0.014	-0.022	17.207	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	65	LEU	0	0.018	0.021	13.745	0.020	0.020	0.000	0.000	0.000	0.000
25	A	66	ASN	0	0.022	0.003	11.719	-0.079	-0.079	0.000	0.000	0.000	0.000
26	A	67	LEU	0	-0.026	-0.028	8.984	0.059	0.059	0.000	0.000	0.000	0.000
27	A	68	PRO	0	-0.014	-0.006	4.329	0.207	0.324	-0.001	-0.042	-0.074	0.000
28	A	69	LYS	1	0.862	0.944	3.693	0.528	0.839	0.000	-0.043	-0.268	0.000
29	A	70	ASP	-1	-0.871	-0.938	2.550	-8.246	-6.172	0.648	-1.277	-1.445	-0.009
30	A	71	SER	0	-0.012	-0.004	2.560	-2.321	-0.293	0.297	-1.028	-1.297	-0.008
31	A	72	GLN	0	0.002	0.019	4.654	0.418	0.441	-0.001	-0.011	-0.011	0.000
32	A	73	LEU	0	0.030	0.018	6.952	0.173	0.173	0.000	0.000	0.000	0.000
33	A	74	SER	0	0.085	0.060	9.858	0.109	0.109	0.000	0.000	0.000	0.000
34	A	75	TYR	0	0.011	-0.009	13.427	0.011	0.011	0.000	0.000	0.000	0.000
35	A	76	LEU	0	-0.040	0.007	16.401	0.032	0.032	0.000	0.000	0.000	0.000
36	A	77	ASP	-1	-0.853	-0.930	12.481	-0.424	-0.424	0.000	0.000	0.000	0.000
37	A	78	LEU	0	-0.050	-0.023	13.911	0.021	0.021	0.000	0.000	0.000	0.000
38	A	79	GLY	0	0.020	0.002	15.810	0.035	0.035	0.000	0.000	0.000	0.000
39	A	80	ASN	0	-0.013	-0.012	17.730	0.051	0.051	0.000	0.000	0.000	0.000
40	A	81	LYS	1	0.939	0.977	11.946	0.606	0.606	0.000	0.000	0.000	0.000
41	A	82	VAL	0	0.006	0.010	18.370	0.029	0.029	0.000	0.000	0.000	0.000
42	A	83	LYS	1	0.829	0.889	20.917	0.229	0.229	0.000	0.000	0.000	0.000
43	A	84	ALA	0	-0.003	0.005	20.572	0.020	0.020	0.000	0.000	0.000	0.000
44	A	85	LEU	0	0.019	0.014	19.455	0.016	0.016	0.000	0.000	0.000	0.000
45	A	86	LEU	0	-0.023	-0.007	23.266	0.018	0.018	0.000	0.000	0.000	0.000
46	A	87	TYR	0	-0.044	-0.012	26.196	0.016	0.016	0.000	0.000	0.000	0.000
47	A	88	ASP	-1	-0.884	-0.949	23.789	-0.111	-0.111	0.000	0.000	0.000	0.000
48	A	89	GLU	-1	-0.828	-0.896	24.777	-0.144	-0.144	0.000	0.000	0.000	0.000
49	A	90	ARG	1	0.741	0.853	27.960	0.134	0.134	0.000	0.000	0.000	0.000
50	A	91	GLY	0	0.022	0.037	30.135	0.006	0.006	0.000	0.000	0.000	0.000
51	A	92	VAL	0	-0.088	-0.043	29.613	0.005	0.005	0.000	0.000	0.000	0.000
52	A	93	THR	0	0.080	0.034	29.670	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	94	PRO	0	0.059	0.001	28.491	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	95	GLU	-1	-0.862	-0.920	30.648	-0.076	-0.076	0.000	0.000	0.000	0.000
55	A	96	LYS	1	0.928	0.961	33.112	0.093	0.093	0.000	0.000	0.000	0.000
56	A	97	ILE	0	0.030	0.014	27.687	0.000	0.000	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.882	0.925	31.941	0.089	0.089	0.000	0.000	0.000	0.000
58	A	99	ASN	0	-0.035	-0.028	34.095	0.001	0.001	0.000	0.000	0.000	0.000
59	A	100	ALA	0	-0.026	0.026	33.566	0.003	0.003	0.000	0.000	0.000	0.000
60	A	101	LYS	1	0.940	0.980	35.649	0.093	0.093	0.000	0.000	0.000	0.000
61	A	102	SER	0	-0.036	-0.037	32.679	0.001	0.001	0.000	0.000	0.000	0.000
62	A	103	ALA	0	0.021	0.010	29.193	0.004	0.004	0.000	0.000	0.000	0.000
63	A	104	VAL	0	0.009	0.023	26.436	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	105	TYR	0	0.056	0.022	18.725	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	106	THR	0	-0.002	-0.004	23.373	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	107	ILE	0	0.006	0.006	17.123	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	108	THR	0	-0.007	0.006	19.637	0.033	0.033	0.000	0.000	0.000	0.000
68	A	109	TRP	0	0.036	0.002	14.178	-0.064	-0.064	0.000	0.000	0.000	0.000
69	A	110	LYS	1	0.823	0.882	12.269	0.798	0.798	0.000	0.000	0.000	0.000
70	A	111	ASP	-1	-0.830	-0.885	17.863	-0.313	-0.313	0.000	0.000	0.000	0.000
71	A	112	GLY	0	-0.015	0.000	20.679	0.035	0.035	0.000	0.000	0.000	0.000
72	A	113	SER	0	-0.035	-0.034	21.190	0.021	0.021	0.000	0.000	0.000	0.000
73	A	114	LYS	1	0.881	0.906	21.907	0.235	0.235	0.000	0.000	0.000	0.000
74	A	115	LYS	1	0.913	0.970	19.304	0.369	0.369	0.000	0.000	0.000	0.000
75	A	116	GLU	-1	-0.921	-0.951	22.583	-0.199	-0.199	0.000	0.000	0.000	0.000
76	A	117	VAL	0	-0.036	-0.022	20.570	0.001	0.001	0.000	0.000	0.000	0.000
77	A	118	ASP	-1	-0.796	-0.900	24.025	-0.153	-0.153	0.000	0.000	0.000	0.000
78	A	119	LEU	0	0.001	-0.014	23.294	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	120	LYS	1	0.766	0.890	26.751	0.121	0.121	0.000	0.000	0.000	0.000
80	A	121	LYS	1	0.839	0.913	28.427	0.160	0.160	0.000	0.000	0.000	0.000
81	A	122	ASP	-1	-0.791	-0.855	24.249	-0.207	-0.207	0.000	0.000	0.000	0.000
82	A	123	SER	0	-0.024	-0.031	24.730	0.014	0.014	0.000	0.000	0.000	0.000
83	A	124	TYR	0	-0.012	-0.008	18.834	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	125	THR	0	0.023	0.005	19.016	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	126	ALA	0	0.049	0.019	17.827	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	127	ASN	0	-0.068	-0.024	16.415	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	128	LEU	0	0.042	0.007	11.085	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	129	PHE	0	-0.061	-0.039	11.321	0.062	0.062	0.000	0.000	0.000	0.000
89	A	130	ASP	-1	-0.755	-0.863	9.131	-1.470	-1.470	0.000	0.000	0.000	0.000
90	A	131	SER	0	-0.020	-0.030	6.594	0.169	0.169	0.000	0.000	0.000	0.000
91	A	132	ASN	0	-0.009	-0.018	6.719	-0.028	-0.028	0.000	0.000	0.000	0.000
92	A	133	SER	0	-0.024	-0.027	9.741	0.257	0.257	0.000	0.000	0.000	0.000
93	A	134	ILE	0	-0.042	-0.006	12.164	0.144	0.144	0.000	0.000	0.000	0.000
94	A	135	LYS	1	0.917	0.977	13.955	0.280	0.280	0.000	0.000	0.000	0.000
95	A	136	GLN	0	-0.061	-0.044	16.797	0.012	0.012	0.000	0.000	0.000	0.000
96	A	137	ILE	0	-0.028	-0.007	15.729	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	138	ASP	-1	-0.808	-0.848	20.047	-0.219	-0.219	0.000	0.000	0.000	0.000
98	A	139	ILE	0	0.000	-0.008	21.523	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	140	ASN	0	-0.037	-0.027	25.142	0.023	0.023	0.000	0.000	0.000	0.000
100	A	141	VAL	0	0.039	0.018	28.739	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	142	LYS	1	0.916	0.976	31.230	0.138	0.138	0.000	0.000	0.000	0.000
102	A	143	THR	0	0.056	0.004	34.956	0.000	0.000	0.000	0.000	0.000	0.000
103	A	144	LYS	1	0.910	0.960	37.120	0.098	0.098	0.000	0.000	0.000	0.000

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