FMO DATABASE

FMODB ID: 5JQQZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1217383.4888
FMO2-HF: Nuclear repulsion	1155977.156383
FMO2-HF: Total energy	-61406.332417
FMO2-MP2: Total energy	-61579.209545

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.
-42.368	-30.055	14.745	-8.5	-18.56	-0.057

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 : -0.043 / 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	L	14	HIS	0	0.005	-0.026	2.990	-3.783	-1.133	3.679	-2.662	-3.667	0.003
4	L	15	PHE	0	0.015	-0.009	2.799	-2.153	-4.320	8.976	0.231	-7.041	-0.012
5	L	16	PRO	0	0.001	0.008	4.511	-2.240	-2.034	0.027	-0.042	-0.191	0.001
6	L	17	GLY	0	0.067	0.037	7.795	-0.597	-0.597	0.000	0.000	0.000	0.000
7	L	18	ASN	0	-0.040	-0.021	6.505	0.180	0.180	0.000	0.000	0.000	0.000
8	L	19	LEU	0	0.043	0.026	5.042	-0.194	-0.194	0.000	0.000	0.000	0.000
9	L	20	PRO	0	0.037	0.018	8.629	-0.227	-0.227	0.000	0.000	0.000	0.000
10	L	21	ASN	0	-0.052	-0.019	12.187	-0.018	-0.018	0.000	0.000	0.000	0.000
11	L	22	MET	0	0.023	0.020	8.897	-0.058	-0.058	0.000	0.000	0.000	0.000
12	L	23	LEU	0	-0.012	-0.007	11.007	-0.153	-0.153	0.000	0.000	0.000	0.000
13	L	24	ARG	1	0.859	0.920	13.511	0.166	0.166	0.000	0.000	0.000	0.000
14	L	25	ASP	-1	-0.821	-0.912	14.380	-0.213	-0.213	0.000	0.000	0.000	0.000
15	L	26	LEU	0	0.017	0.011	14.080	0.005	0.005	0.000	0.000	0.000	0.000
16	L	27	ARG	1	0.939	0.972	16.334	0.667	0.667	0.000	0.000	0.000	0.000
17	L	28	ASP	-1	-0.813	-0.894	19.429	-0.192	-0.192	0.000	0.000	0.000	0.000
18	L	29	ALA	0	-0.009	0.019	19.592	0.044	0.044	0.000	0.000	0.000	0.000
19	L	30	PHE	0	0.044	0.016	20.802	0.029	0.029	0.000	0.000	0.000	0.000
20	L	31	SER	0	-0.072	-0.055	22.546	0.045	0.045	0.000	0.000	0.000	0.000
21	L	32	ARG	1	0.869	0.924	23.974	0.270	0.270	0.000	0.000	0.000	0.000
22	L	33	VAL	0	0.039	0.013	24.804	0.015	0.015	0.000	0.000	0.000	0.000
23	L	34	LYS	1	0.907	0.974	26.168	0.328	0.328	0.000	0.000	0.000	0.000
24	L	35	THR	0	0.014	-0.009	27.720	-0.005	-0.005	0.000	0.000	0.000	0.000
25	L	36	PHE	0	0.040	0.032	30.796	0.013	0.013	0.000	0.000	0.000	0.000
26	L	37	PHE	0	0.042	0.003	27.664	0.002	0.002	0.000	0.000	0.000	0.000
27	L	38	GLN	0	-0.052	-0.035	28.559	0.009	0.009	0.000	0.000	0.000	0.000
28	L	39	MET	0	-0.018	0.003	31.782	0.019	0.019	0.000	0.000	0.000	0.000
29	L	40	LYS	1	0.788	0.887	33.574	0.295	0.295	0.000	0.000	0.000	0.000
30	L	41	ASP	-1	-0.911	-0.954	31.743	-0.349	-0.349	0.000	0.000	0.000	0.000
31	L	42	GLN	0	-0.072	-0.043	34.215	0.021	0.021	0.000	0.000	0.000	0.000
32	L	43	LEU	0	-0.023	0.002	34.821	0.016	0.016	0.000	0.000	0.000	0.000
33	L	44	ASP	-1	-0.902	-0.945	34.157	-0.269	-0.269	0.000	0.000	0.000	0.000
34	L	45	ASN	0	-0.092	-0.049	32.777	0.005	0.005	0.000	0.000	0.000	0.000
35	L	46	LEU	0	0.041	0.026	26.174	-0.014	-0.014	0.000	0.000	0.000	0.000
36	L	47	LEU	0	0.021	0.019	26.626	0.001	0.001	0.000	0.000	0.000	0.000
37	L	48	LEU	0	0.006	-0.010	21.593	-0.005	-0.005	0.000	0.000	0.000	0.000
38	L	49	LYS	1	0.893	0.938	25.227	0.431	0.431	0.000	0.000	0.000	0.000
39	L	50	GLU	-1	-0.886	-0.945	24.215	-0.502	-0.502	0.000	0.000	0.000	0.000
40	L	51	SER	0	0.027	0.008	23.590	-0.022	-0.022	0.000	0.000	0.000	0.000
41	L	52	LEU	0	0.049	0.034	19.797	-0.029	-0.029	0.000	0.000	0.000	0.000
42	L	53	LEU	0	-0.026	-0.007	18.046	-0.116	-0.116	0.000	0.000	0.000	0.000
43	L	54	GLU	-1	-0.780	-0.889	19.186	-0.654	-0.654	0.000	0.000	0.000	0.000
44	L	55	ASP	-1	-0.894	-0.947	20.005	-0.759	-0.759	0.000	0.000	0.000	0.000
45	L	56	PHE	0	-0.116	-0.073	15.483	-0.144	-0.144	0.000	0.000	0.000	0.000
46	L	57	LYS	1	0.763	0.867	15.275	0.485	0.485	0.000	0.000	0.000	0.000
47	L	58	GLY	0	0.045	0.045	17.483	0.050	0.050	0.000	0.000	0.000	0.000
48	L	59	TYR	0	-0.034	-0.029	16.856	-0.131	-0.131	0.000	0.000	0.000	0.000
49	L	60	LEU	0	0.029	0.009	17.327	-0.013	-0.013	0.000	0.000	0.000	0.000
50	L	61	GLY	0	0.029	0.031	15.015	-0.088	-0.088	0.000	0.000	0.000	0.000
51	L	62	CYS	0	-0.082	-0.028	8.224	-0.041	-0.041	0.000	0.000	0.000	0.000
52	L	63	GLN	0	-0.022	-0.014	12.315	-0.335	-0.335	0.000	0.000	0.000	0.000
53	L	64	ALA	0	0.074	0.041	14.987	-0.024	-0.024	0.000	0.000	0.000	0.000
54	L	65	LEU	0	-0.013	-0.003	10.481	-0.006	-0.006	0.000	0.000	0.000	0.000
55	L	66	SER	0	-0.026	-0.041	11.476	-0.231	-0.231	0.000	0.000	0.000	0.000
56	L	67	GLU	-1	-0.871	-0.918	13.142	-0.954	-0.954	0.000	0.000	0.000	0.000
57	L	68	MET	0	0.001	0.009	16.592	0.119	0.119	0.000	0.000	0.000	0.000
58	L	69	ILE	0	-0.043	-0.031	11.283	0.023	0.023	0.000	0.000	0.000	0.000
59	L	70	GLN	0	-0.034	-0.004	14.924	-0.165	-0.165	0.000	0.000	0.000	0.000
60	L	71	PHE	0	0.070	0.037	17.130	0.097	0.097	0.000	0.000	0.000	0.000
61	L	72	TYR	0	-0.017	-0.021	18.287	0.099	0.099	0.000	0.000	0.000	0.000
62	L	73	LEU	0	-0.058	-0.043	14.460	0.060	0.060	0.000	0.000	0.000	0.000
63	L	74	GLU	-1	-0.921	-0.955	18.337	-0.959	-0.959	0.000	0.000	0.000	0.000
64	L	75	GLU	-1	-0.902	-0.943	21.274	-0.619	-0.619	0.000	0.000	0.000	0.000
65	L	76	VAL	0	-0.022	-0.010	23.101	0.051	0.051	0.000	0.000	0.000	0.000
66	L	77	MET	0	-0.052	-0.016	19.673	0.010	0.010	0.000	0.000	0.000	0.000
67	L	78	PRO	0	0.032	0.022	22.205	0.065	0.065	0.000	0.000	0.000	0.000
68	L	79	GLN	0	-0.014	-0.006	25.166	0.032	0.032	0.000	0.000	0.000	0.000
69	L	80	ALA	0	0.022	0.010	26.774	0.040	0.040	0.000	0.000	0.000	0.000
70	L	81	GLU	-1	-0.879	-0.948	23.060	-0.535	-0.535	0.000	0.000	0.000	0.000
71	L	82	ASN	0	-0.059	-0.045	27.889	0.033	0.033	0.000	0.000	0.000	0.000
72	L	83	GLN	0	-0.023	0.011	30.715	0.008	0.008	0.000	0.000	0.000	0.000
73	L	84	ASP	-1	-0.771	-0.867	31.948	-0.274	-0.274	0.000	0.000	0.000	0.000
74	L	85	PRO	0	0.005	-0.015	31.893	-0.012	-0.012	0.000	0.000	0.000	0.000
75	L	86	ASP	-1	-0.913	-0.947	32.102	-0.232	-0.232	0.000	0.000	0.000	0.000
76	L	87	ILE	0	-0.032	-0.016	28.538	0.004	0.004	0.000	0.000	0.000	0.000
77	L	88	LYS	1	0.915	0.977	27.557	0.316	0.316	0.000	0.000	0.000	0.000
78	L	89	ALA	0	0.027	0.007	26.160	-0.037	-0.037	0.000	0.000	0.000	0.000
79	L	90	HIS	0	0.013	0.023	24.772	-0.044	-0.044	0.000	0.000	0.000	0.000
80	L	91	VAL	0	0.017	0.005	23.572	-0.040	-0.040	0.000	0.000	0.000	0.000
81	L	92	ASN	0	-0.036	-0.014	21.980	-0.067	-0.067	0.000	0.000	0.000	0.000
82	L	93	SER	0	-0.014	-0.025	20.272	-0.056	-0.056	0.000	0.000	0.000	0.000
83	L	94	LEU	0	-0.042	-0.015	18.680	-0.051	-0.051	0.000	0.000	0.000	0.000
84	L	95	GLY	0	0.066	0.024	17.607	-0.134	-0.134	0.000	0.000	0.000	0.000
85	L	96	GLU	-1	-0.850	-0.917	15.902	-0.985	-0.985	0.000	0.000	0.000	0.000
86	L	97	ASN	0	-0.063	-0.028	14.325	-0.139	-0.139	0.000	0.000	0.000	0.000
87	L	98	LEU	0	0.035	0.018	12.964	-0.250	-0.250	0.000	0.000	0.000	0.000
88	L	99	LYS	1	0.880	0.933	11.778	0.434	0.434	0.000	0.000	0.000	0.000
89	L	100	THR	0	-0.037	-0.035	10.049	-0.569	-0.569	0.000	0.000	0.000	0.000
90	L	101	LEU	0	-0.027	-0.016	8.672	-0.526	-0.526	0.000	0.000	0.000	0.000
91	L	102	ARG	1	0.849	0.904	7.155	1.084	1.084	0.000	0.000	0.000	0.000
92	L	103	LEU	0	-0.019	-0.015	6.045	-2.236	-2.236	0.000	0.000	0.000	0.000
93	L	104	ARG	1	0.842	0.915	4.029	-4.689	-4.236	0.012	-0.157	-0.307	-0.001
94	L	105	LEU	0	0.026	0.013	2.814	-8.987	-5.787	0.432	-1.389	-2.244	-0.015
95	L	106	ARG	1	0.904	0.955	2.427	-7.994	-3.126	1.398	-3.339	-2.927	-0.034
98	L	110	ARG	1	0.958	0.972	3.903	-0.527	1.356	-0.012	-0.896	-0.976	0.001
99	L	111	PHE	0	-0.015	-0.004	2.725	0.734	1.811	0.235	-0.227	-1.085	0.000
100	L	112	LEU	0	0.030	0.009	5.556	0.714	0.714	0.000	0.000	0.000	0.000
101	L	113	PRO	0	0.006	-0.005	6.977	0.001	0.001	0.000	0.000	0.000	0.000
102	L	115	GLU	-1	-0.721	-0.828	7.925	-3.781	-3.781	0.000	0.000	0.000	0.000
103	L	116	ASN	0	-0.104	-0.059	4.362	-0.779	-0.636	-0.002	-0.019	-0.122	0.000
104	L	117	LYS	1	0.877	0.927	8.159	1.015	1.015	0.000	0.000	0.000	0.000
105	L	118	SER	0	0.054	0.025	10.393	0.381	0.381	0.000	0.000	0.000	0.000
106	L	119	LYS	1	0.966	0.974	11.150	-1.109	-1.109	0.000	0.000	0.000	0.000
107	L	120	ALA	0	0.050	0.025	12.984	-0.043	-0.043	0.000	0.000	0.000	0.000
108	L	121	VAL	0	0.062	0.031	16.165	-0.028	-0.028	0.000	0.000	0.000	0.000
109	L	122	GLU	-1	-0.763	-0.866	14.588	-0.289	-0.289	0.000	0.000	0.000	0.000
110	L	123	GLN	0	-0.020	-0.022	16.069	0.071	0.071	0.000	0.000	0.000	0.000
111	L	124	VAL	0	0.038	0.025	18.698	-0.012	-0.012	0.000	0.000	0.000	0.000
112	L	125	LYS	1	0.903	0.950	17.272	0.248	0.248	0.000	0.000	0.000	0.000
113	L	126	ASN	0	-0.012	-0.011	18.812	0.019	0.019	0.000	0.000	0.000	0.000
114	L	127	ALA	0	-0.003	0.001	22.034	0.000	0.000	0.000	0.000	0.000	0.000
115	L	128	PHE	0	0.022	0.015	24.846	-0.007	-0.007	0.000	0.000	0.000	0.000
116	L	129	ASN	0	-0.027	-0.036	23.296	-0.006	-0.006	0.000	0.000	0.000	0.000
117	L	130	LYS	1	0.876	0.937	21.957	-0.177	-0.177	0.000	0.000	0.000	0.000
118	L	131	LEU	0	0.003	0.018	27.962	0.005	0.005	0.000	0.000	0.000	0.000
119	L	132	GLN	0	0.000	0.002	29.917	-0.007	-0.007	0.000	0.000	0.000	0.000
120	L	133	GLU	-1	-0.752	-0.864	31.623	0.000	0.000	0.000	0.000	0.000	0.000
121	L	134	LYS	1	0.807	0.884	34.063	-0.027	-0.027	0.000	0.000	0.000	0.000
122	L	135	GLY	0	0.001	0.007	30.234	0.006	0.006	0.000	0.000	0.000	0.000
123	L	136	ILE	0	-0.011	-0.008	30.915	-0.005	-0.005	0.000	0.000	0.000	0.000
124	L	137	TYR	0	0.005	0.000	32.514	-0.006	-0.006	0.000	0.000	0.000	0.000
125	L	138	LYS	1	0.874	0.934	29.643	-0.062	-0.062	0.000	0.000	0.000	0.000
126	L	139	ALA	0	0.021	0.003	28.911	0.001	0.001	0.000	0.000	0.000	0.000
127	L	140	MET	0	-0.024	-0.013	30.379	-0.012	-0.012	0.000	0.000	0.000	0.000
128	L	141	SER	0	-0.086	-0.048	33.519	0.001	0.001	0.000	0.000	0.000	0.000
129	L	142	GLU	-1	-0.827	-0.891	29.554	0.058	0.058	0.000	0.000	0.000	0.000
130	L	143	PHE	0	-0.007	-0.009	29.747	-0.005	-0.005	0.000	0.000	0.000	0.000
131	L	144	ASP	-1	-0.827	-0.921	31.197	-0.020	-0.020	0.000	0.000	0.000	0.000
132	L	145	ILE	0	-0.011	0.004	28.057	-0.002	-0.002	0.000	0.000	0.000	0.000
133	L	146	PHE	0	-0.060	-0.025	23.776	-0.005	-0.005	0.000	0.000	0.000	0.000
134	L	147	ILE	0	0.034	0.011	27.169	-0.016	-0.016	0.000	0.000	0.000	0.000
135	L	148	ASN	0	0.032	0.012	29.201	-0.014	-0.014	0.000	0.000	0.000	0.000
136	L	149	TYR	0	-0.068	-0.033	23.849	0.014	0.014	0.000	0.000	0.000	0.000
137	L	150	ILE	0	-0.027	-0.005	24.907	-0.014	-0.014	0.000	0.000	0.000	0.000
138	L	151	GLU	-1	-0.893	-0.948	26.120	-0.094	-0.094	0.000	0.000	0.000	0.000
139	L	152	ALA	0	-0.005	0.010	25.813	-0.003	-0.003	0.000	0.000	0.000	0.000
140	L	153	TYR	0	-0.047	-0.023	19.001	-0.014	-0.014	0.000	0.000	0.000	0.000
141	L	154	MET	0	-0.036	-0.018	23.722	-0.023	-0.023	0.000	0.000	0.000	0.000
142	L	155	THR	0	-0.058	-0.023	26.202	-0.006	-0.006	0.000	0.000	0.000	0.000
143	L	156	MET	0	-0.118	-0.060	19.812	0.005	0.005	0.000	0.000	0.000	0.000

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