FMO DATABASE

FMODB ID: 948Z2

Calculation Name: 1Y14-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y14

Chain ID: A

ChEMBL ID:

UniProt ID: P20433

Base Structure: X-ray

Registration Date: 2023-06-22

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1120794.412604
FMO2-HF: Nuclear repulsion	1068315.088686
FMO2-HF: Total energy	-52479.323919
FMO2-MP2: Total energy	-52634.350232

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:46:GLU)

Summations of interaction energy for fragment #1(A:46:GLU)

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.
18.833	23.731	0.905	-2.441	-3.362	0.003

Interaction energy analysis for fragmet #1(A:46:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.973 / q_NPA : -0.999

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	A	48	ILE	0	0.060	0.038	2.816	2.702	7.557	0.906	-2.416	-3.345	0.003
4	A	49	ALA	0	-0.059	-0.026	4.677	-7.101	-7.058	-0.001	-0.025	-0.017	0.000
5	A	50	LEU	0	0.013	0.005	8.162	0.020	0.020	0.000	0.000	0.000	0.000
6	A	51	ASN	0	0.026	0.025	11.030	-1.729	-1.729	0.000	0.000	0.000	0.000
7	A	52	LEU	0	0.022	-0.021	14.508	0.130	0.130	0.000	0.000	0.000	0.000
8	A	53	SER	0	0.027	0.013	17.338	-0.546	-0.546	0.000	0.000	0.000	0.000
9	A	54	GLU	-1	-0.813	-0.917	12.264	24.276	24.276	0.000	0.000	0.000	0.000
10	A	55	ALA	0	0.013	0.023	14.236	0.229	0.229	0.000	0.000	0.000	0.000
11	A	56	ARG	1	0.778	0.857	15.055	-14.078	-14.078	0.000	0.000	0.000	0.000
12	A	57	LEU	0	-0.057	-0.026	16.979	-0.685	-0.685	0.000	0.000	0.000	0.000
13	A	58	VAL	0	0.065	0.037	12.350	-0.471	-0.471	0.000	0.000	0.000	0.000
14	A	59	ILE	0	-0.012	-0.004	15.437	-0.459	-0.459	0.000	0.000	0.000	0.000
15	A	60	LYS	1	0.892	0.938	17.845	-13.317	-13.317	0.000	0.000	0.000	0.000
16	A	61	GLU	-1	-0.926	-0.948	16.338	17.796	17.796	0.000	0.000	0.000	0.000
17	A	62	ALA	0	0.047	0.030	16.827	-0.561	-0.561	0.000	0.000	0.000	0.000
18	A	63	LEU	0	-0.018	-0.026	18.847	-0.689	-0.689	0.000	0.000	0.000	0.000
19	A	64	VAL	0	-0.047	-0.022	22.230	-0.867	-0.867	0.000	0.000	0.000	0.000
20	A	65	GLU	-1	-0.954	-0.979	19.357	15.408	15.408	0.000	0.000	0.000	0.000
21	A	66	ARG	1	0.929	0.975	19.349	-14.926	-14.926	0.000	0.000	0.000	0.000
22	A	67	ARG	1	0.945	0.972	23.969	-11.410	-11.410	0.000	0.000	0.000	0.000
23	A	68	ARG	1	0.916	0.961	24.877	-12.645	-12.645	0.000	0.000	0.000	0.000
24	A	69	ALA	0	-0.021	-0.032	24.918	-0.410	-0.410	0.000	0.000	0.000	0.000
25	A	70	PHE	0	-0.021	-0.002	25.149	-0.150	-0.150	0.000	0.000	0.000	0.000
26	A	71	LYS	1	0.958	0.968	29.369	-10.174	-10.174	0.000	0.000	0.000	0.000
27	A	72	ARG	1	0.870	0.965	25.873	-11.943	-11.943	0.000	0.000	0.000	0.000
28	A	73	SER	0	-0.005	-0.019	29.826	-0.281	-0.281	0.000	0.000	0.000	0.000
29	A	74	GLN	0	0.000	0.030	31.368	0.190	0.190	0.000	0.000	0.000	0.000
30	A	118	THR	0	-0.014	-0.017	31.722	0.026	0.026	0.000	0.000	0.000	0.000
31	A	119	ARG	1	0.888	0.925	25.538	-11.376	-11.376	0.000	0.000	0.000	0.000
32	A	120	GLU	-1	-0.777	-0.919	30.564	9.468	9.468	0.000	0.000	0.000	0.000
33	A	121	LYS	1	0.982	0.982	33.187	-8.375	-8.375	0.000	0.000	0.000	0.000
34	A	122	GLU	-1	-0.803	-0.871	25.210	12.343	12.343	0.000	0.000	0.000	0.000
35	A	123	LEU	0	-0.014	-0.018	29.014	0.233	0.233	0.000	0.000	0.000	0.000
36	A	124	GLU	-1	-0.917	-0.943	30.642	8.687	8.687	0.000	0.000	0.000	0.000
37	A	125	SER	0	-0.077	-0.042	29.596	-0.078	-0.078	0.000	0.000	0.000	0.000
38	A	126	ILE	0	-0.031	-0.005	26.694	0.274	0.274	0.000	0.000	0.000	0.000
39	A	127	ASP	-1	-0.889	-0.933	28.716	9.985	9.985	0.000	0.000	0.000	0.000
40	A	128	VAL	0	0.012	0.011	31.312	0.046	0.046	0.000	0.000	0.000	0.000
41	A	129	LEU	0	-0.046	-0.036	24.519	0.001	0.001	0.000	0.000	0.000	0.000
42	A	130	LEU	0	0.011	0.006	24.603	0.273	0.273	0.000	0.000	0.000	0.000
43	A	131	GLU	-1	-0.952	-0.944	27.701	9.326	9.326	0.000	0.000	0.000	0.000
44	A	132	GLN	0	0.003	0.008	29.921	0.268	0.268	0.000	0.000	0.000	0.000
45	A	133	THR	0	-0.068	-0.048	24.881	0.314	0.314	0.000	0.000	0.000	0.000
46	A	134	THR	0	-0.103	-0.079	23.444	0.575	0.575	0.000	0.000	0.000	0.000
47	A	135	GLY	0	0.020	0.008	25.556	-0.314	-0.314	0.000	0.000	0.000	0.000
48	A	136	GLY	0	0.073	0.051	27.504	-0.380	-0.380	0.000	0.000	0.000	0.000
49	A	137	ASN	0	-0.037	-0.008	25.320	-0.210	-0.210	0.000	0.000	0.000	0.000
50	A	138	ASN	0	0.007	-0.015	20.651	0.006	0.006	0.000	0.000	0.000	0.000
51	A	139	LYS	1	1.029	1.014	24.663	-10.540	-10.540	0.000	0.000	0.000	0.000
52	A	140	ASP	-1	-0.860	-0.919	20.769	13.129	13.129	0.000	0.000	0.000	0.000
53	A	141	LEU	0	-0.015	-0.002	20.000	0.253	0.253	0.000	0.000	0.000	0.000
54	A	142	LYS	1	1.005	1.000	22.047	-9.998	-9.998	0.000	0.000	0.000	0.000
55	A	143	ASN	0	-0.038	-0.031	24.722	-0.221	-0.221	0.000	0.000	0.000	0.000
56	A	144	THR	0	0.009	0.002	19.052	0.127	0.127	0.000	0.000	0.000	0.000
57	A	145	MET	0	0.016	0.013	22.054	0.113	0.113	0.000	0.000	0.000	0.000
58	A	146	GLN	0	0.030	0.018	23.410	-0.082	-0.082	0.000	0.000	0.000	0.000
59	A	147	TYR	0	0.017	0.021	20.076	-0.082	-0.082	0.000	0.000	0.000	0.000
60	A	148	LEU	0	0.024	0.003	18.341	-0.138	-0.138	0.000	0.000	0.000	0.000
61	A	149	THR	0	-0.041	-0.013	22.118	-0.043	-0.043	0.000	0.000	0.000	0.000
62	A	150	ASN	0	-0.035	-0.036	25.262	-0.432	-0.432	0.000	0.000	0.000	0.000
63	A	151	PHE	0	-0.016	-0.003	23.283	-0.303	-0.303	0.000	0.000	0.000	0.000
64	A	152	SER	0	-0.054	-0.023	21.059	0.583	0.583	0.000	0.000	0.000	0.000
65	A	153	ARG	1	0.927	0.994	21.761	-13.467	-13.467	0.000	0.000	0.000	0.000
66	A	154	PHE	0	0.022	0.008	19.632	-0.278	-0.278	0.000	0.000	0.000	0.000
67	A	155	ARG	1	0.861	0.910	21.481	-11.105	-11.105	0.000	0.000	0.000	0.000
68	A	156	ASP	-1	-0.786	-0.851	23.515	12.460	12.460	0.000	0.000	0.000	0.000
69	A	157	GLN	0	0.029	-0.014	16.754	0.551	0.551	0.000	0.000	0.000	0.000
70	A	158	GLU	-1	-0.965	-0.969	20.026	12.574	12.574	0.000	0.000	0.000	0.000
71	A	159	THR	0	0.020	-0.014	21.543	0.354	0.354	0.000	0.000	0.000	0.000
72	A	160	VAL	0	-0.027	-0.006	16.131	0.443	0.443	0.000	0.000	0.000	0.000
73	A	161	GLY	0	-0.013	-0.006	16.818	0.909	0.909	0.000	0.000	0.000	0.000
74	A	162	ALA	0	0.034	0.006	17.533	0.687	0.687	0.000	0.000	0.000	0.000
75	A	163	VAL	0	0.035	0.017	16.946	0.189	0.189	0.000	0.000	0.000	0.000
76	A	164	ILE	0	-0.036	-0.009	12.483	0.494	0.494	0.000	0.000	0.000	0.000
77	A	165	GLN	0	-0.082	-0.031	14.771	0.204	0.204	0.000	0.000	0.000	0.000
78	A	166	LEU	0	0.016	0.012	16.791	0.281	0.281	0.000	0.000	0.000	0.000
79	A	167	LEU	0	0.038	0.015	15.334	-0.079	-0.079	0.000	0.000	0.000	0.000
80	A	168	LYS	1	0.941	1.003	11.418	-23.385	-23.385	0.000	0.000	0.000	0.000
81	A	169	SER	0	-0.133	-0.063	13.964	0.353	0.353	0.000	0.000	0.000	0.000
82	A	170	THR	0	0.012	-0.019	15.991	-0.509	-0.509	0.000	0.000	0.000	0.000
83	A	171	GLY	0	-0.032	-0.006	14.549	-0.613	-0.613	0.000	0.000	0.000	0.000
84	A	172	LEU	0	-0.022	-0.003	14.538	0.388	0.388	0.000	0.000	0.000	0.000
85	A	173	HIS	0	0.001	0.011	7.859	1.232	1.232	0.000	0.000	0.000	0.000
86	A	174	PRO	0	0.067	0.025	6.462	-1.599	-1.599	0.000	0.000	0.000	0.000
87	A	175	PHE	0	0.024	-0.016	6.615	-1.261	-1.261	0.000	0.000	0.000	0.000
88	A	176	GLU	-1	-0.754	-0.837	10.673	18.301	18.301	0.000	0.000	0.000	0.000
89	A	177	VAL	0	0.010	0.009	11.507	-1.291	-1.291	0.000	0.000	0.000	0.000
90	A	178	ALA	0	0.013	-0.001	11.197	-1.222	-1.222	0.000	0.000	0.000	0.000
91	A	179	GLN	0	-0.017	-0.018	13.165	-2.163	-2.163	0.000	0.000	0.000	0.000
92	A	180	LEU	0	0.029	0.021	16.183	-1.033	-1.033	0.000	0.000	0.000	0.000
93	A	181	GLY	0	-0.009	0.008	16.397	-0.767	-0.767	0.000	0.000	0.000	0.000
94	A	182	SER	0	-0.102	-0.068	16.240	-0.335	-0.335	0.000	0.000	0.000	0.000
95	A	183	LEU	0	-0.033	-0.019	18.894	-0.703	-0.703	0.000	0.000	0.000	0.000
96	A	184	ALA	0	-0.024	-0.003	21.722	0.156	0.156	0.000	0.000	0.000	0.000
97	A	185	CYS	0	-0.043	-0.017	23.631	-0.086	-0.086	0.000	0.000	0.000	0.000
98	A	186	ASP	-1	-0.893	-0.945	26.297	10.376	10.376	0.000	0.000	0.000	0.000
99	A	187	THR	0	-0.051	-0.026	29.015	-0.183	-0.183	0.000	0.000	0.000	0.000
100	A	188	ALA	0	0.017	-0.010	26.661	0.401	0.401	0.000	0.000	0.000	0.000
101	A	189	ASP	-1	-0.906	-0.951	26.503	10.684	10.684	0.000	0.000	0.000	0.000
102	A	190	GLU	-1	-0.841	-0.866	26.642	11.238	11.238	0.000	0.000	0.000	0.000
103	A	191	ALA	0	0.039	0.002	22.719	0.376	0.376	0.000	0.000	0.000	0.000
104	A	192	LYS	1	0.739	0.852	22.739	-11.673	-11.673	0.000	0.000	0.000	0.000
105	A	193	THR	0	-0.049	-0.055	23.844	0.125	0.125	0.000	0.000	0.000	0.000
106	A	194	LEU	0	-0.061	-0.035	22.751	0.169	0.169	0.000	0.000	0.000	0.000
107	A	195	ILE	0	-0.058	-0.021	17.340	0.782	0.782	0.000	0.000	0.000	0.000
108	A	196	PRO	0	0.076	0.034	20.119	0.212	0.212	0.000	0.000	0.000	0.000
109	A	197	SER	0	-0.144	-0.104	16.452	-0.246	-0.246	0.000	0.000	0.000	0.000
110	A	198	LEU	0	0.046	0.004	17.846	0.395	0.395	0.000	0.000	0.000	0.000
111	A	199	ASN	0	0.033	0.015	20.097	-0.431	-0.431	0.000	0.000	0.000	0.000
112	A	200	ASN	0	-0.057	-0.028	22.235	-0.724	-0.724	0.000	0.000	0.000	0.000
113	A	201	LYS	1	0.800	0.906	14.561	-19.555	-19.555	0.000	0.000	0.000	0.000
114	A	202	ILE	0	0.030	0.028	20.605	0.226	0.226	0.000	0.000	0.000	0.000
115	A	203	SER	0	0.033	0.029	22.831	-0.223	-0.223	0.000	0.000	0.000	0.000
116	A	204	ASP	-1	-0.793	-0.906	26.161	11.265	11.265	0.000	0.000	0.000	0.000
117	A	205	ASP	-1	-0.974	-0.986	28.261	10.340	10.340	0.000	0.000	0.000	0.000
118	A	206	GLU	-1	-0.851	-0.947	23.655	12.798	12.798	0.000	0.000	0.000	0.000
119	A	207	LEU	0	-0.027	-0.012	21.970	0.449	0.449	0.000	0.000	0.000	0.000
120	A	208	GLU	-1	-0.819	-0.915	24.736	10.658	10.658	0.000	0.000	0.000	0.000
121	A	209	ARG	1	0.893	0.967	23.695	-12.810	-12.810	0.000	0.000	0.000	0.000
122	A	210	ILE	0	-0.023	-0.012	20.341	0.088	0.088	0.000	0.000	0.000	0.000
123	A	211	LEU	0	0.018	0.015	23.472	0.251	0.251	0.000	0.000	0.000	0.000
124	A	212	LYS	1	0.903	0.953	25.407	-10.163	-10.163	0.000	0.000	0.000	0.000
125	A	213	GLU	-1	-0.903	-0.960	23.923	11.996	11.996	0.000	0.000	0.000	0.000
126	A	214	LEU	0	-0.043	-0.027	19.916	0.145	0.145	0.000	0.000	0.000	0.000
127	A	215	SER	0	-0.047	-0.027	24.013	-0.055	-0.055	0.000	0.000	0.000	0.000
128	A	216	ASN	0	-0.023	-0.008	27.375	-0.463	-0.463	0.000	0.000	0.000	0.000
129	A	217	LEU	0	-0.015	0.001	22.200	-0.059	-0.059	0.000	0.000	0.000	0.000
130	A	218	GLU	-1	-0.911	-0.947	25.505	11.687	11.687	0.000	0.000	0.000	0.000
131	A	219	THR	0	-0.022	-0.006	25.825	-0.211	-0.211	0.000	0.000	0.000	0.000
132	A	220	LEU	0	0.053	0.024	27.732	-0.136	-0.136	0.000	0.000	0.000	0.000
133	A	221	TYR	0	-0.102	-0.048	27.327	-0.343	-0.343	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:46:GLU)