FMO DATABASE

FMODB ID: 4JKKN

Calculation Name: 1Y6K-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y6K

Chain ID: L

ChEMBL ID:

UniProt ID: Q13651

Base Structure: X-ray

Registration Date: 2023-09-23

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1217487.909661
FMO2-HF: Nuclear repulsion	1156082.470012
FMO2-HF: Total energy	-61405.439649
FMO2-MP2: Total energy	-61578.527054

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(L:12:CYS)

Summations of interaction energy for fragment #1(L:12:CYS)

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.
-38.695	-29.346	14.614	-8.167	-15.796	-0.03

Interaction energy analysis for fragmet #1(L:12:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.008

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	L	14	HIS	0	-0.004	-0.017	2.572	-4.379	-4.257	7.479	-3.191	-4.410	0.007
4	L	15	PHE	0	0.014	-0.021	2.890	-2.833	-3.018	6.483	-0.464	-5.834	-0.010
5	L	16	PRO	0	-0.010	0.006	4.364	-1.652	-1.644	0.033	0.111	-0.151	0.001
6	L	17	GLY	0	0.071	0.032	7.558	-0.553	-0.553	0.000	0.000	0.000	0.000
7	L	18	ASN	0	-0.057	-0.024	6.989	-0.050	-0.050	0.000	0.000	0.000	0.000
8	L	19	LEU	0	0.040	0.018	4.813	-0.151	-0.151	0.000	0.000	0.000	0.000
9	L	20	PRO	0	0.056	0.040	8.567	-0.178	-0.178	0.000	0.000	0.000	0.000
10	L	21	ASN	0	-0.034	-0.014	12.236	-0.018	-0.018	0.000	0.000	0.000	0.000
11	L	22	MET	0	0.010	0.005	9.122	-0.117	-0.117	0.000	0.000	0.000	0.000
12	L	23	LEU	0	0.004	0.012	11.357	-0.099	-0.099	0.000	0.000	0.000	0.000
13	L	24	ARG	1	0.839	0.911	13.785	0.332	0.332	0.000	0.000	0.000	0.000
14	L	25	ASP	-1	-0.834	-0.922	14.868	-0.481	-0.481	0.000	0.000	0.000	0.000
15	L	26	LEU	0	-0.006	0.005	14.100	0.019	0.019	0.000	0.000	0.000	0.000
16	L	27	ARG	1	0.945	0.960	16.740	0.789	0.789	0.000	0.000	0.000	0.000
17	L	28	ASP	-1	-0.833	-0.902	19.601	-0.331	-0.331	0.000	0.000	0.000	0.000
18	L	29	ALA	0	-0.004	0.015	19.713	0.058	0.058	0.000	0.000	0.000	0.000
19	L	30	PHE	0	0.049	0.018	21.074	0.037	0.037	0.000	0.000	0.000	0.000
20	L	31	SER	0	-0.066	-0.046	22.786	0.056	0.056	0.000	0.000	0.000	0.000
21	L	32	ARG	1	0.875	0.928	24.122	0.382	0.382	0.000	0.000	0.000	0.000
22	L	33	VAL	0	0.019	0.003	25.067	0.021	0.021	0.000	0.000	0.000	0.000
23	L	34	LYS	1	0.898	0.973	26.572	0.383	0.383	0.000	0.000	0.000	0.000
24	L	35	THR	0	0.028	-0.006	28.101	-0.002	-0.002	0.000	0.000	0.000	0.000
25	L	36	PHE	0	0.049	0.031	30.997	0.013	0.013	0.000	0.000	0.000	0.000
26	L	37	PHE	0	0.058	0.009	27.413	0.008	0.008	0.000	0.000	0.000	0.000
27	L	38	GLN	0	-0.039	-0.019	28.475	0.016	0.016	0.000	0.000	0.000	0.000
28	L	39	MET	0	-0.042	0.000	31.988	0.017	0.017	0.000	0.000	0.000	0.000
29	L	40	LYS	1	0.815	0.896	33.758	0.337	0.337	0.000	0.000	0.000	0.000
30	L	41	ASP	-1	-0.961	-0.979	31.788	-0.385	-0.385	0.000	0.000	0.000	0.000
31	L	42	GLN	0	-0.039	-0.021	34.298	0.014	0.014	0.000	0.000	0.000	0.000
32	L	43	LEU	0	-0.033	0.005	34.955	0.017	0.017	0.000	0.000	0.000	0.000
33	L	44	ASP	-1	-0.869	-0.930	34.914	-0.286	-0.286	0.000	0.000	0.000	0.000
34	L	45	ASN	0	-0.103	-0.040	32.600	0.011	0.011	0.000	0.000	0.000	0.000
35	L	46	LEU	0	0.025	0.013	26.477	-0.011	-0.011	0.000	0.000	0.000	0.000
36	L	47	LEU	0	0.031	0.007	26.985	0.010	0.010	0.000	0.000	0.000	0.000
37	L	48	LEU	0	0.006	0.000	21.737	-0.009	-0.009	0.000	0.000	0.000	0.000
38	L	49	LYS	1	0.898	0.936	25.096	0.434	0.434	0.000	0.000	0.000	0.000
39	L	50	GLU	-1	-0.896	-0.950	24.173	-0.514	-0.514	0.000	0.000	0.000	0.000
40	L	51	SER	0	0.026	0.008	24.132	-0.007	-0.007	0.000	0.000	0.000	0.000
41	L	52	LEU	0	0.036	0.020	19.962	-0.024	-0.024	0.000	0.000	0.000	0.000
42	L	53	LEU	0	-0.036	-0.009	18.540	-0.105	-0.105	0.000	0.000	0.000	0.000
43	L	54	GLU	-1	-0.749	-0.880	19.487	-0.645	-0.645	0.000	0.000	0.000	0.000
44	L	55	ASP	-1	-0.871	-0.933	20.005	-0.758	-0.758	0.000	0.000	0.000	0.000
45	L	56	PHE	0	-0.129	-0.071	15.638	-0.142	-0.142	0.000	0.000	0.000	0.000
46	L	57	LYS	1	0.754	0.862	15.425	0.492	0.492	0.000	0.000	0.000	0.000
47	L	58	GLY	0	0.047	0.048	17.707	0.078	0.078	0.000	0.000	0.000	0.000
48	L	59	TYR	0	-0.009	-0.013	17.114	-0.118	-0.118	0.000	0.000	0.000	0.000
49	L	60	LEU	0	0.019	0.000	17.501	0.008	0.008	0.000	0.000	0.000	0.000
50	L	61	GLY	0	0.009	0.016	14.936	-0.093	-0.093	0.000	0.000	0.000	0.000
51	L	62	CYS	0	-0.085	-0.024	8.221	-0.065	-0.065	0.000	0.000	0.000	0.000
52	L	63	GLN	0	-0.024	-0.032	12.474	-0.297	-0.297	0.000	0.000	0.000	0.000
53	L	64	ALA	0	0.071	0.042	15.106	0.002	0.002	0.000	0.000	0.000	0.000
54	L	65	LEU	0	-0.024	-0.014	10.463	-0.033	-0.033	0.000	0.000	0.000	0.000
55	L	66	SER	0	-0.027	-0.042	11.749	-0.264	-0.264	0.000	0.000	0.000	0.000
56	L	67	GLU	-1	-0.839	-0.898	13.197	-0.983	-0.983	0.000	0.000	0.000	0.000
57	L	68	MET	0	0.012	0.027	16.465	0.112	0.112	0.000	0.000	0.000	0.000
58	L	69	ILE	0	-0.048	-0.023	11.025	0.012	0.012	0.000	0.000	0.000	0.000
59	L	70	GLN	0	-0.023	-0.015	14.951	-0.135	-0.135	0.000	0.000	0.000	0.000
60	L	71	PHE	0	0.047	0.031	16.932	0.107	0.107	0.000	0.000	0.000	0.000
61	L	72	TYR	0	-0.016	-0.025	18.333	0.095	0.095	0.000	0.000	0.000	0.000
62	L	73	LEU	0	-0.057	-0.042	14.476	0.058	0.058	0.000	0.000	0.000	0.000
63	L	74	GLU	-1	-0.925	-0.949	18.729	-0.979	-0.979	0.000	0.000	0.000	0.000
64	L	75	GLU	-1	-0.897	-0.950	21.296	-0.628	-0.628	0.000	0.000	0.000	0.000
65	L	76	VAL	0	-0.033	-0.016	23.006	0.052	0.052	0.000	0.000	0.000	0.000
66	L	77	MET	0	-0.049	-0.026	20.062	0.006	0.006	0.000	0.000	0.000	0.000
67	L	78	PRO	0	0.028	0.026	22.512	0.070	0.070	0.000	0.000	0.000	0.000
68	L	79	GLN	0	-0.016	-0.013	25.382	0.038	0.038	0.000	0.000	0.000	0.000
69	L	80	ALA	0	0.002	0.009	27.022	0.041	0.041	0.000	0.000	0.000	0.000
70	L	81	GLU	-1	-0.878	-0.946	23.313	-0.620	-0.620	0.000	0.000	0.000	0.000
71	L	82	ASN	0	-0.041	-0.031	28.101	0.039	0.039	0.000	0.000	0.000	0.000
72	L	83	GLN	0	-0.005	0.005	30.602	0.010	0.010	0.000	0.000	0.000	0.000
73	L	84	ASP	-1	-0.811	-0.886	32.068	-0.313	-0.313	0.000	0.000	0.000	0.000
74	L	85	PRO	0	0.015	-0.019	31.801	-0.014	-0.014	0.000	0.000	0.000	0.000
75	L	86	ASP	-1	-0.932	-0.944	32.161	-0.284	-0.284	0.000	0.000	0.000	0.000
76	L	87	ILE	0	-0.003	-0.014	28.688	-0.001	-0.001	0.000	0.000	0.000	0.000
77	L	88	LYS	1	0.900	0.980	27.756	0.368	0.368	0.000	0.000	0.000	0.000
78	L	89	ALA	0	-0.017	-0.002	26.431	-0.035	-0.035	0.000	0.000	0.000	0.000
79	L	90	HIS	0	0.040	0.009	24.975	-0.062	-0.062	0.000	0.000	0.000	0.000
80	L	91	VAL	0	0.002	0.000	23.753	-0.043	-0.043	0.000	0.000	0.000	0.000
81	L	92	ASN	0	-0.017	-0.002	21.777	-0.094	-0.094	0.000	0.000	0.000	0.000
82	L	93	SER	0	-0.025	-0.024	20.354	-0.063	-0.063	0.000	0.000	0.000	0.000
83	L	94	LEU	0	-0.027	0.001	18.809	-0.081	-0.081	0.000	0.000	0.000	0.000
84	L	95	GLY	0	0.076	0.025	17.585	-0.141	-0.141	0.000	0.000	0.000	0.000
85	L	96	GLU	-1	-0.845	-0.909	16.025	-1.192	-1.192	0.000	0.000	0.000	0.000
86	L	97	ASN	0	-0.055	-0.032	14.368	-0.210	-0.210	0.000	0.000	0.000	0.000
87	L	98	LEU	0	0.050	0.034	12.905	-0.266	-0.266	0.000	0.000	0.000	0.000
88	L	99	LYS	1	0.879	0.939	11.634	0.532	0.532	0.000	0.000	0.000	0.000
89	L	100	THR	0	-0.049	-0.051	10.029	-0.587	-0.587	0.000	0.000	0.000	0.000
90	L	101	LEU	0	-0.032	-0.018	8.449	-0.361	-0.361	0.000	0.000	0.000	0.000
91	L	102	ARG	1	0.846	0.897	7.136	1.086	1.086	0.000	0.000	0.000	0.000
92	L	103	LEU	0	-0.036	-0.021	6.042	-2.319	-2.319	0.000	0.000	0.000	0.000
93	L	104	ARG	1	0.900	0.937	3.982	-4.231	-3.917	0.009	-0.119	-0.204	-0.001
94	L	105	LEU	0	-0.002	0.007	3.060	-6.656	-4.215	0.129	-1.117	-1.453	-0.010
95	L	106	ARG	1	0.906	0.956	2.792	-4.173	-0.157	0.372	-2.389	-2.000	-0.022
98	L	110	ARG	1	0.977	0.977	3.842	-2.870	-1.238	-0.015	-0.813	-0.805	0.005
99	L	111	PHE	0	-0.022	0.025	2.775	1.086	1.982	0.126	-0.178	-0.843	0.000
100	L	112	LEU	0	0.053	0.013	5.187	1.151	1.151	0.000	0.000	0.000	0.000
101	L	113	PRO	0	-0.005	-0.010	6.833	0.008	0.008	0.000	0.000	0.000	0.000
102	L	115	GLU	-1	-0.722	-0.821	8.198	-3.734	-3.734	0.000	0.000	0.000	0.000
103	L	116	ASN	0	-0.100	-0.060	4.449	-0.859	-0.754	-0.002	-0.007	-0.096	0.000
104	L	117	LYS	1	0.871	0.934	8.305	0.929	0.929	0.000	0.000	0.000	0.000
105	L	118	SER	0	0.029	0.010	10.280	0.378	0.378	0.000	0.000	0.000	0.000
106	L	119	LYS	1	1.001	0.988	11.160	-1.451	-1.451	0.000	0.000	0.000	0.000
107	L	120	ALA	0	0.044	0.026	12.963	-0.076	-0.076	0.000	0.000	0.000	0.000
108	L	121	VAL	0	0.042	0.009	16.018	-0.051	-0.051	0.000	0.000	0.000	0.000
109	L	122	GLU	-1	-0.833	-0.895	14.419	-0.188	-0.188	0.000	0.000	0.000	0.000
110	L	123	GLN	0	0.000	-0.016	16.263	0.014	0.014	0.000	0.000	0.000	0.000
111	L	124	VAL	0	0.036	0.027	18.645	-0.031	-0.031	0.000	0.000	0.000	0.000
112	L	125	LYS	1	1.000	1.005	18.002	0.202	0.202	0.000	0.000	0.000	0.000
113	L	126	ASN	0	-0.032	-0.020	18.569	-0.008	-0.008	0.000	0.000	0.000	0.000
114	L	127	ALA	0	-0.027	-0.016	22.112	-0.010	-0.010	0.000	0.000	0.000	0.000
115	L	128	PHE	0	0.010	0.008	24.367	-0.012	-0.012	0.000	0.000	0.000	0.000
116	L	129	ASN	0	-0.010	-0.019	23.351	-0.015	-0.015	0.000	0.000	0.000	0.000
117	L	130	LYS	1	0.887	0.939	22.094	-0.222	-0.222	0.000	0.000	0.000	0.000
118	L	131	LEU	0	-0.026	0.013	27.743	0.005	0.005	0.000	0.000	0.000	0.000
119	L	132	GLN	0	0.008	-0.007	29.902	-0.010	-0.010	0.000	0.000	0.000	0.000
120	L	133	GLU	-1	-0.815	-0.878	31.541	0.013	0.013	0.000	0.000	0.000	0.000
121	L	134	LYS	1	0.852	0.898	33.842	-0.044	-0.044	0.000	0.000	0.000	0.000
122	L	135	GLY	0	0.015	0.003	30.537	0.008	0.008	0.000	0.000	0.000	0.000
123	L	136	ILE	0	-0.002	-0.005	31.055	-0.002	-0.002	0.000	0.000	0.000	0.000
124	L	137	TYR	0	0.006	-0.009	32.618	-0.005	-0.005	0.000	0.000	0.000	0.000
125	L	138	LYS	1	0.877	0.946	29.953	-0.102	-0.102	0.000	0.000	0.000	0.000
126	L	139	ALA	0	0.005	-0.002	28.734	0.005	0.005	0.000	0.000	0.000	0.000
127	L	140	MET	0	-0.005	-0.007	30.073	-0.008	-0.008	0.000	0.000	0.000	0.000
128	L	141	SER	0	-0.011	-0.006	33.073	-0.003	-0.003	0.000	0.000	0.000	0.000
129	L	142	GLU	-1	-0.857	-0.907	29.066	0.113	0.113	0.000	0.000	0.000	0.000
130	L	143	PHE	0	-0.007	-0.001	30.227	0.001	0.001	0.000	0.000	0.000	0.000
131	L	144	ASP	-1	-0.847	-0.926	30.927	0.032	0.032	0.000	0.000	0.000	0.000
132	L	145	ILE	0	0.021	0.013	27.887	0.005	0.005	0.000	0.000	0.000	0.000
133	L	146	PHE	0	-0.068	-0.028	23.704	-0.001	-0.001	0.000	0.000	0.000	0.000
134	L	147	ILE	0	0.024	-0.001	27.265	-0.007	-0.007	0.000	0.000	0.000	0.000
135	L	148	ASN	0	0.043	0.022	29.333	-0.014	-0.014	0.000	0.000	0.000	0.000
136	L	149	TYR	0	-0.082	-0.032	23.903	0.024	0.024	0.000	0.000	0.000	0.000
137	L	150	ILE	0	-0.046	-0.023	24.906	-0.006	-0.006	0.000	0.000	0.000	0.000
138	L	151	GLU	-1	-0.916	-0.963	25.943	-0.026	-0.026	0.000	0.000	0.000	0.000
139	L	152	ALA	0	-0.009	-0.005	25.562	-0.001	-0.001	0.000	0.000	0.000	0.000
140	L	153	TYR	0	-0.090	-0.047	18.874	-0.010	-0.010	0.000	0.000	0.000	0.000
141	L	154	MET	0	0.004	-0.010	23.581	-0.012	-0.012	0.000	0.000	0.000	0.000
142	L	155	THR	0	-0.096	-0.020	25.817	-0.014	-0.014	0.000	0.000	0.000	0.000
143	L	156	MET	0	-0.060	-0.026	19.808	0.034	0.034	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:12:CYS)