FMO DATABASE

FMODB ID: 94YJ2

Calculation Name: 1YKE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YKE

Chain ID: B

ChEMBL ID:

UniProt ID: P47822

Base Structure: X-ray

Registration Date: 2023-06-21

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-734105.771038
FMO2-HF: Nuclear repulsion	685604.03216
FMO2-HF: Total energy	-48501.738878
FMO2-MP2: Total energy	-48642.872646

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(B:3:ASP)

Summations of interaction energy for fragment #1(B:3:ASP)

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.
49.626	54.755	0.455	-2.177	-3.407	-0.003

Interaction energy analysis for fragmet #1(B:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.908 / q_NPA : -0.957

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	B	5	LEU	0	0.075	0.037	3.799	-5.686	-3.672	-0.023	-0.900	-1.092	0.003
4	B	6	THR	0	0.056	0.019	2.788	-4.909	-2.730	0.474	-1.077	-1.576	-0.007
5	B	7	GLN	0	0.056	0.027	3.593	-12.794	-11.937	0.005	-0.196	-0.666	0.001
6	B	8	LEU	0	-0.055	-0.005	5.236	-5.005	-4.926	-0.001	-0.004	-0.073	0.000
7	B	9	GLN	0	0.019	-0.017	7.452	0.574	0.574	0.000	0.000	0.000	0.000
8	B	10	ILE	0	0.020	0.036	5.586	-1.584	-1.584	0.000	0.000	0.000	0.000
9	B	11	CYS	0	-0.104	-0.059	8.811	-3.720	-3.720	0.000	0.000	0.000	0.000
10	B	12	LEU	0	-0.037	-0.020	10.900	-2.092	-2.092	0.000	0.000	0.000	0.000
11	B	13	ASP	-1	-0.870	-0.935	12.284	20.975	20.975	0.000	0.000	0.000	0.000
12	B	14	GLN	0	0.045	0.018	12.186	-2.865	-2.865	0.000	0.000	0.000	0.000
13	B	15	MET	0	-0.004	0.009	15.711	-1.518	-1.518	0.000	0.000	0.000	0.000
14	B	16	THR	0	0.036	0.021	16.206	-1.164	-1.164	0.000	0.000	0.000	0.000
15	B	17	GLU	-1	-0.947	-0.981	16.849	18.101	18.101	0.000	0.000	0.000	0.000
16	B	18	GLN	0	0.022	-0.001	19.685	-0.739	-0.739	0.000	0.000	0.000	0.000
17	B	19	PHE	0	-0.055	-0.040	21.276	-0.840	-0.840	0.000	0.000	0.000	0.000
18	B	20	CYS	0	-0.047	-0.019	22.979	-0.714	-0.714	0.000	0.000	0.000	0.000
19	B	21	ALA	0	-0.053	-0.017	23.370	-0.633	-0.633	0.000	0.000	0.000	0.000
20	B	22	THR	0	0.039	0.023	25.255	-0.538	-0.538	0.000	0.000	0.000	0.000
21	B	23	LEU	0	-0.010	-0.010	27.235	-0.398	-0.398	0.000	0.000	0.000	0.000
22	B	24	ASN	0	0.020	0.016	28.252	-0.477	-0.477	0.000	0.000	0.000	0.000
23	B	25	TYR	0	-0.008	-0.004	30.079	-0.501	-0.501	0.000	0.000	0.000	0.000
24	B	26	ILE	0	0.008	-0.020	30.833	-0.356	-0.356	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.891	-0.933	32.568	9.359	9.359	0.000	0.000	0.000	0.000
26	B	28	LYS	1	0.786	0.884	31.570	-10.368	-10.368	0.000	0.000	0.000	0.000
27	B	29	ASN	0	-0.023	-0.007	34.517	-0.321	-0.321	0.000	0.000	0.000	0.000
28	B	30	HIS	0	0.024	0.002	37.652	-0.051	-0.051	0.000	0.000	0.000	0.000
29	B	31	GLY	0	0.021	0.016	36.351	-0.146	-0.146	0.000	0.000	0.000	0.000
30	B	32	PHE	0	-0.013	-0.013	37.438	-0.030	-0.030	0.000	0.000	0.000	0.000
31	B	33	GLU	-1	-0.971	-0.983	38.712	7.068	7.068	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.828	0.943	38.468	-8.238	-8.238	0.000	0.000	0.000	0.000
33	B	35	LEU	0	-0.036	-0.006	38.166	-0.076	-0.076	0.000	0.000	0.000	0.000
34	B	48	THR	0	-0.002	-0.006	42.442	-0.082	-0.082	0.000	0.000	0.000	0.000
35	B	49	VAL	0	-0.050	-0.031	41.955	0.132	0.132	0.000	0.000	0.000	0.000
36	B	50	VAL	0	0.048	0.044	37.310	-0.133	-0.133	0.000	0.000	0.000	0.000
37	B	51	PRO	0	0.002	-0.007	40.620	-0.107	-0.107	0.000	0.000	0.000	0.000
38	B	52	PRO	0	-0.031	-0.037	40.685	0.191	0.191	0.000	0.000	0.000	0.000
39	B	53	GLU	-1	-0.942	-0.951	39.805	7.973	7.973	0.000	0.000	0.000	0.000
40	B	54	GLU	-1	-0.815	-0.925	36.438	8.906	8.906	0.000	0.000	0.000	0.000
41	B	55	PHE	0	-0.004	0.016	35.527	0.349	0.349	0.000	0.000	0.000	0.000
42	B	56	SER	0	0.054	0.032	34.929	0.247	0.247	0.000	0.000	0.000	0.000
43	B	57	ASN	0	0.004	0.001	34.472	0.069	0.069	0.000	0.000	0.000	0.000
44	B	58	THR	0	0.034	0.014	30.818	0.342	0.342	0.000	0.000	0.000	0.000
45	B	59	ILE	0	-0.025	-0.029	30.556	0.422	0.422	0.000	0.000	0.000	0.000
46	B	60	ASP	-1	-0.921	-0.970	30.188	9.997	9.997	0.000	0.000	0.000	0.000
47	B	61	GLU	-1	-0.976	-0.990	27.584	11.677	11.677	0.000	0.000	0.000	0.000
48	B	62	LEU	0	-0.028	-0.002	25.849	0.596	0.596	0.000	0.000	0.000	0.000
49	B	63	SER	0	-0.011	-0.008	25.274	0.657	0.657	0.000	0.000	0.000	0.000
50	B	64	THR	0	-0.012	-0.006	25.770	0.537	0.537	0.000	0.000	0.000	0.000
51	B	65	ASP	-1	-0.931	-0.964	21.233	15.718	15.718	0.000	0.000	0.000	0.000
52	B	66	ILE	0	0.026	0.003	21.346	0.982	0.982	0.000	0.000	0.000	0.000
53	B	67	ILE	0	-0.040	-0.006	21.413	0.538	0.538	0.000	0.000	0.000	0.000
54	B	68	LEU	0	-0.038	-0.007	19.025	0.367	0.367	0.000	0.000	0.000	0.000
55	B	69	LYS	1	0.943	0.972	15.242	-19.235	-19.235	0.000	0.000	0.000	0.000
56	B	70	THR	0	0.041	0.012	16.968	0.935	0.935	0.000	0.000	0.000	0.000
57	B	71	ARG	1	0.932	0.971	18.385	-13.879	-13.879	0.000	0.000	0.000	0.000
58	B	72	GLN	0	-0.064	-0.045	14.440	-0.340	-0.340	0.000	0.000	0.000	0.000
59	B	73	ILE	0	0.049	0.021	12.955	1.189	1.189	0.000	0.000	0.000	0.000
60	B	74	ASN	0	-0.002	0.003	13.874	0.521	0.521	0.000	0.000	0.000	0.000
61	B	75	LYS	1	0.986	0.988	14.823	-15.820	-15.820	0.000	0.000	0.000	0.000
62	B	76	LEU	0	-0.036	-0.007	9.268	0.560	0.560	0.000	0.000	0.000	0.000
63	B	77	ILE	0	0.009	-0.008	11.064	1.510	1.510	0.000	0.000	0.000	0.000
64	B	78	ASP	-1	-0.962	-0.971	12.830	17.247	17.247	0.000	0.000	0.000	0.000
65	B	79	SER	0	-0.071	-0.047	11.032	-0.327	-0.327	0.000	0.000	0.000	0.000
66	B	80	LEU	0	-0.055	-0.012	7.721	2.329	2.329	0.000	0.000	0.000	0.000
67	B	81	PRO	0	-0.068	-0.032	6.254	-1.430	-1.430	0.000	0.000	0.000	0.000
68	B	82	GLY	0	-0.028	-0.035	9.431	0.800	0.800	0.000	0.000	0.000	0.000
69	B	83	VAL	0	-0.015	0.011	11.775	-0.915	-0.915	0.000	0.000	0.000	0.000
70	B	84	ASP	-1	-0.892	-0.948	14.199	15.436	15.436	0.000	0.000	0.000	0.000
71	B	85	VAL	0	-0.058	-0.016	14.769	-0.694	-0.694	0.000	0.000	0.000	0.000
72	B	86	SER	0	0.041	0.034	16.393	0.309	0.309	0.000	0.000	0.000	0.000
73	B	87	ALA	0	0.090	0.026	16.264	0.615	0.615	0.000	0.000	0.000	0.000
74	B	88	GLU	-1	-0.933	-0.976	17.345	11.657	11.657	0.000	0.000	0.000	0.000
75	B	89	GLU	-1	-0.963	-0.996	18.192	14.192	14.192	0.000	0.000	0.000	0.000
76	B	90	GLN	0	-0.036	-0.016	11.748	-0.170	-0.170	0.000	0.000	0.000	0.000
77	B	91	LEU	0	0.052	0.009	16.190	0.024	0.024	0.000	0.000	0.000	0.000
78	B	92	ARG	1	0.963	1.002	17.906	-12.532	-12.532	0.000	0.000	0.000	0.000
79	B	93	LYS	1	0.969	0.989	15.585	-16.507	-16.507	0.000	0.000	0.000	0.000
80	B	94	ILE	0	-0.026	-0.016	14.185	0.244	0.244	0.000	0.000	0.000	0.000
81	B	95	ASP	-1	-0.809	-0.905	16.657	11.941	11.941	0.000	0.000	0.000	0.000
82	B	96	MET	0	-0.055	-0.035	19.414	-0.405	-0.405	0.000	0.000	0.000	0.000
83	B	97	LEU	0	-0.079	-0.043	15.125	-0.292	-0.292	0.000	0.000	0.000	0.000
84	B	98	GLN	0	0.026	0.012	18.243	0.333	0.333	0.000	0.000	0.000	0.000
85	B	99	LYS	1	0.934	0.970	20.052	-11.494	-11.494	0.000	0.000	0.000	0.000
86	B	100	LYS	1	0.957	0.971	21.589	-13.022	-13.022	0.000	0.000	0.000	0.000
87	B	101	LEU	0	-0.023	0.004	17.771	-0.023	-0.023	0.000	0.000	0.000	0.000
88	B	102	VAL	0	0.002	0.005	21.944	-0.102	-0.102	0.000	0.000	0.000	0.000
89	B	103	GLU	-1	-0.939	-0.963	24.893	10.396	10.396	0.000	0.000	0.000	0.000
90	B	104	VAL	0	0.028	0.010	23.437	-0.224	-0.224	0.000	0.000	0.000	0.000
91	B	105	GLU	-1	-0.935	-0.965	23.828	12.304	12.304	0.000	0.000	0.000	0.000
92	B	106	ASP	-1	-0.897	-0.950	26.243	9.887	9.887	0.000	0.000	0.000	0.000
93	B	107	GLU	-1	-0.975	-0.994	28.593	10.055	10.055	0.000	0.000	0.000	0.000
94	B	108	LYS	1	0.893	0.960	24.067	-12.463	-12.463	0.000	0.000	0.000	0.000
95	B	109	ILE	0	-0.013	-0.018	28.973	-0.342	-0.342	0.000	0.000	0.000	0.000
96	B	110	GLU	-1	-0.945	-0.971	31.113	8.183	8.183	0.000	0.000	0.000	0.000
97	B	111	ALA	0	-0.012	-0.003	31.577	-0.271	-0.271	0.000	0.000	0.000	0.000
98	B	112	ILE	0	-0.006	-0.007	28.810	-0.210	-0.210	0.000	0.000	0.000	0.000
99	B	113	LYS	1	0.938	0.978	33.199	-8.871	-8.871	0.000	0.000	0.000	0.000
100	B	114	LYS	1	0.937	0.956	36.444	-8.424	-8.424	0.000	0.000	0.000	0.000
101	B	115	LYS	1	0.984	0.999	32.494	-9.656	-9.656	0.000	0.000	0.000	0.000
102	B	116	GLU	-1	-0.876	-0.944	35.892	8.389	8.389	0.000	0.000	0.000	0.000
103	B	117	LYS	1	0.859	0.939	38.410	-7.320	-7.320	0.000	0.000	0.000	0.000
104	B	118	LEU	0	-0.013	-0.008	39.620	-0.181	-0.181	0.000	0.000	0.000	0.000
105	B	119	LEU	0	0.001	-0.006	38.529	-0.113	-0.113	0.000	0.000	0.000	0.000
106	B	120	ARG	1	0.981	0.991	40.664	-7.647	-7.647	0.000	0.000	0.000	0.000
107	B	121	HIS	0	-0.085	-0.024	43.956	-0.196	-0.196	0.000	0.000	0.000	0.000
108	B	122	VAL	0	0.004	-0.007	43.255	-0.147	-0.147	0.000	0.000	0.000	0.000
109	B	123	ASP	-1	-0.859	-0.940	43.154	7.275	7.275	0.000	0.000	0.000	0.000
110	B	124	SER	0	-0.044	-0.014	46.283	-0.141	-0.141	0.000	0.000	0.000	0.000
111	B	125	LEU	0	-0.034	-0.023	49.048	-0.115	-0.115	0.000	0.000	0.000	0.000
112	B	126	ILE	0	-0.026	-0.028	46.117	-0.103	-0.103	0.000	0.000	0.000	0.000
113	B	127	GLU	-1	-0.968	-0.977	50.144	6.218	6.218	0.000	0.000	0.000	0.000
114	B	128	ASP	-1	-0.927	-0.960	51.590	5.774	5.774	0.000	0.000	0.000	0.000
115	B	129	PHE	0	-0.128	-0.056	52.424	-0.123	-0.123	0.000	0.000	0.000	0.000
116	B	130	VAL	0	-0.055	-0.017	52.618	-0.033	-0.033	0.000	0.000	0.000	0.000
117	B	131	ASP	-1	-0.906	-0.935	55.622	5.325	5.325	0.000	0.000	0.000	0.000
118	B	132	GLY	0	-0.055	-0.050	58.549	0.019	0.019	0.000	0.000	0.000	0.000
119	B	133	ILE	0	-0.050	-0.010	57.970	0.034	0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:ASP)