FMO DATABASE

FMODB ID: YVLL2

Calculation Name: 5AP8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5AP8

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UWV6

Base Structure: X-ray

Registration Date: 2023-09-24

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1546761.48221
FMO2-HF: Nuclear repulsion	1487316.260401
FMO2-HF: Total energy	-59445.221809
FMO2-MP2: Total energy	-59623.754431

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:1:MET)

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

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.
-20.348	-9.252	5.249	-5.512	-10.831	-0.035

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.001

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	3	VAL	0	0.020	0.007	3.530	-1.760	0.165	0.013	-0.895	-1.043	0.002
4	A	4	TYR	0	-0.024	-0.020	5.671	0.300	0.300	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.015	0.007	9.196	-0.124	-0.124	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.029	-0.025	12.323	0.084	0.084	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.880	-0.940	15.597	-0.166	-0.166	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.055	-0.023	18.732	0.041	0.041	0.000	0.000	0.000	0.000
9	A	18	GLY	0	0.070	0.032	15.546	0.002	0.002	0.000	0.000	0.000	0.000
10	A	19	LYS	1	0.942	0.952	15.188	0.173	0.173	0.000	0.000	0.000	0.000
11	A	20	LYS	1	0.912	0.974	13.744	0.506	0.506	0.000	0.000	0.000	0.000
12	A	21	LEU	0	0.082	0.020	8.752	0.064	0.064	0.000	0.000	0.000	0.000
13	A	22	VAL	0	0.036	0.042	10.574	0.033	0.033	0.000	0.000	0.000	0.000
14	A	23	LYS	1	0.918	0.967	12.876	0.209	0.209	0.000	0.000	0.000	0.000
15	A	24	LEU	0	-0.078	-0.059	10.925	0.072	0.072	0.000	0.000	0.000	0.000
16	A	25	LYS	1	0.974	0.987	9.712	-0.598	-0.598	0.000	0.000	0.000	0.000
17	A	26	ILE	0	0.003	0.016	5.164	0.231	0.231	0.000	0.000	0.000	0.000
18	A	27	ALA	0	0.000	0.007	6.297	-0.299	-0.299	0.000	0.000	0.000	0.000
19	A	28	GLU	-1	-0.941	-0.965	8.890	0.639	0.639	0.000	0.000	0.000	0.000
20	A	29	PHE	0	0.004	-0.006	11.706	-0.071	-0.071	0.000	0.000	0.000	0.000
21	A	30	THR	0	-0.022	-0.026	12.495	0.098	0.098	0.000	0.000	0.000	0.000
22	A	31	ARG	1	0.964	0.979	14.998	-0.107	-0.107	0.000	0.000	0.000	0.000
23	A	32	VAL	0	-0.027	-0.002	15.500	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	33	GLY	0	0.029	0.030	13.170	0.018	0.018	0.000	0.000	0.000	0.000
25	A	34	LYS	1	0.903	0.946	9.772	-0.429	-0.429	0.000	0.000	0.000	0.000
26	A	35	GLY	0	0.024	0.038	7.709	-0.052	-0.052	0.000	0.000	0.000	0.000
27	A	36	VAL	0	0.020	0.007	7.700	-0.066	-0.066	0.000	0.000	0.000	0.000
28	A	37	VAL	0	-0.027	-0.018	8.942	-0.123	-0.123	0.000	0.000	0.000	0.000
29	A	38	LEU	0	0.001	0.000	8.880	0.013	0.013	0.000	0.000	0.000	0.000
30	A	39	ASP	-1	-0.775	-0.892	12.571	-0.098	-0.098	0.000	0.000	0.000	0.000
31	A	40	PRO	0	-0.007	-0.001	16.334	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	41	PHE	0	-0.017	-0.016	19.070	0.012	0.012	0.000	0.000	0.000	0.000
33	A	42	ALA	0	-0.042	0.004	17.742	0.028	0.028	0.000	0.000	0.000	0.000
34	A	43	GLN	0	0.019	-0.007	19.753	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	44	ILE	0	-0.032	-0.003	16.549	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	45	THR	0	-0.030	-0.015	16.261	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	46	LEU	0	-0.046	-0.012	9.027	0.042	0.042	0.000	0.000	0.000	0.000
38	A	47	SER	0	0.028	0.003	12.099	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	48	ASN	0	-0.002	0.009	10.864	0.044	0.044	0.000	0.000	0.000	0.000
40	A	49	LYS	1	0.904	0.935	11.936	0.136	0.136	0.000	0.000	0.000	0.000
41	A	50	ASP	-1	-0.789	-0.876	9.415	0.097	0.097	0.000	0.000	0.000	0.000
42	A	51	LYS	1	0.930	0.949	6.923	-0.233	-0.233	0.000	0.000	0.000	0.000
43	A	52	ASP	-1	-0.838	-0.916	6.008	1.382	1.382	0.000	0.000	0.000	0.000
44	A	53	ILE	0	-0.027	-0.004	7.481	0.537	0.537	0.000	0.000	0.000	0.000
45	A	54	VAL	0	0.030	0.020	2.218	-0.284	0.076	1.151	-0.332	-1.178	0.000
46	A	55	ARG	1	0.938	0.980	2.726	-3.451	-0.669	1.385	-1.580	-2.587	-0.008
47	A	56	ARG	1	0.937	0.971	4.085	-0.396	-0.121	0.000	0.215	-0.490	0.000
48	A	57	ILE	0	-0.057	-0.021	5.857	-0.102	-0.102	0.000	0.000	0.000	0.000
49	A	58	GLY	0	0.022	0.013	3.145	-0.152	0.072	0.040	-0.100	-0.163	0.001
50	A	59	ILE	0	0.021	0.017	3.779	-0.619	-0.245	0.003	-0.035	-0.342	0.000
51	A	60	THR	0	-0.011	-0.027	5.893	-0.065	-0.065	0.000	0.000	0.000	0.000
52	A	61	ILE	0	-0.018	-0.020	9.004	-0.053	-0.053	0.000	0.000	0.000	0.000
53	A	62	VAL	0	0.015	0.010	11.471	0.069	0.069	0.000	0.000	0.000	0.000
54	A	63	ASP	-1	-0.954	-0.972	15.245	-0.342	-0.342	0.000	0.000	0.000	0.000
55	A	64	THR	0	0.021	0.016	16.864	0.037	0.037	0.000	0.000	0.000	0.000
56	A	65	SER	0	-0.030	-0.017	19.123	-0.046	-0.046	0.000	0.000	0.000	0.000
57	A	66	TRP	0	0.043	0.008	19.930	0.012	0.012	0.000	0.000	0.000	0.000
58	A	67	ASN	0	-0.039	-0.032	22.393	0.008	0.008	0.000	0.000	0.000	0.000
59	A	68	ASN	0	0.015	0.001	25.163	0.007	0.007	0.000	0.000	0.000	0.000
60	A	69	THR	0	0.016	0.037	21.621	0.018	0.018	0.000	0.000	0.000	0.000
61	A	70	SER	0	0.034	0.010	23.913	0.014	0.014	0.000	0.000	0.000	0.000
62	A	71	GLN	0	0.049	0.014	23.018	0.001	0.001	0.000	0.000	0.000	0.000
63	A	72	SER	0	-0.075	-0.052	23.681	0.016	0.016	0.000	0.000	0.000	0.000
64	A	73	GLU	-1	-0.809	-0.892	21.204	-0.122	-0.122	0.000	0.000	0.000	0.000
65	A	74	PHE	0	0.003	-0.002	15.970	0.001	0.001	0.000	0.000	0.000	0.000
66	A	75	LYS	1	0.904	0.962	19.595	0.013	0.013	0.000	0.000	0.000	0.000
67	A	76	ASN	0	-0.026	-0.017	21.592	0.010	0.010	0.000	0.000	0.000	0.000
68	A	77	ILE	0	0.007	0.026	15.277	0.027	0.027	0.000	0.000	0.000	0.000
69	A	78	ARG	1	0.967	0.993	16.105	-0.335	-0.335	0.000	0.000	0.000	0.000
70	A	79	GLY	0	0.043	0.016	13.303	0.006	0.006	0.000	0.000	0.000	0.000
71	A	80	GLU	-1	-0.916	-0.958	12.191	0.256	0.256	0.000	0.000	0.000	0.000
72	A	81	HIS	1	0.746	0.843	12.889	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	82	ARG	1	0.840	0.905	11.904	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	83	ARG	1	0.845	0.923	14.408	0.195	0.195	0.000	0.000	0.000	0.000
75	A	84	ILE	0	-0.016	-0.026	12.423	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	85	PRO	0	-0.002	0.014	14.614	0.037	0.037	0.000	0.000	0.000	0.000
77	A	86	ILE	0	0.007	0.014	17.774	-0.044	-0.044	0.000	0.000	0.000	0.000
78	A	87	LEU	0	0.023	0.012	15.062	-0.048	-0.048	0.000	0.000	0.000	0.000
79	A	88	PHE	0	0.006	0.002	19.422	0.041	0.041	0.000	0.000	0.000	0.000
80	A	89	ALA	0	0.030	0.022	19.475	-0.054	-0.054	0.000	0.000	0.000	0.000
81	A	90	GLY	0	0.040	0.006	19.303	0.034	0.034	0.000	0.000	0.000	0.000
82	A	91	ASN	0	-0.027	-0.014	19.550	0.050	0.050	0.000	0.000	0.000	0.000
83	A	92	PRO	0	-0.024	-0.033	21.450	0.022	0.022	0.000	0.000	0.000	0.000
84	A	93	ILE	0	-0.040	-0.016	24.037	0.027	0.027	0.000	0.000	0.000	0.000
85	A	94	HIS	0	-0.004	-0.016	22.820	0.030	0.030	0.000	0.000	0.000	0.000
86	A	95	TYR	0	0.014	0.012	23.925	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	96	GLY	0	0.018	0.014	24.065	0.028	0.028	0.000	0.000	0.000	0.000
88	A	97	ILE	0	-0.026	-0.009	25.165	0.013	0.013	0.000	0.000	0.000	0.000
89	A	98	ALA	0	0.052	0.025	23.108	-0.031	-0.031	0.000	0.000	0.000	0.000
90	A	99	TYR	0	-0.037	-0.045	20.097	0.027	0.027	0.000	0.000	0.000	0.000
91	A	100	LYS	1	0.843	0.934	19.785	0.225	0.225	0.000	0.000	0.000	0.000
92	A	101	LEU	0	-0.033	-0.010	15.291	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	102	SER	0	-0.019	-0.042	16.449	0.008	0.008	0.000	0.000	0.000	0.000
94	A	103	SER	0	0.047	0.003	12.661	-0.085	-0.085	0.000	0.000	0.000	0.000
95	A	104	ILE	0	0.000	-0.006	10.457	-0.111	-0.111	0.000	0.000	0.000	0.000
96	A	105	GLU	-1	-0.741	-0.832	11.282	-0.791	-0.791	0.000	0.000	0.000	0.000
97	A	106	ALA	0	0.057	0.038	12.075	-0.085	-0.085	0.000	0.000	0.000	0.000
98	A	107	LEU	0	-0.011	0.004	5.592	-0.074	-0.074	0.000	0.000	0.000	0.000
99	A	108	ILE	0	-0.023	-0.003	7.431	-0.414	-0.414	0.000	0.000	0.000	0.000
100	A	109	ALA	0	0.032	0.013	9.335	-0.137	-0.137	0.000	0.000	0.000	0.000
101	A	110	THR	0	-0.022	-0.035	6.166	0.145	0.145	0.000	0.000	0.000	0.000
102	A	111	LEU	0	-0.017	-0.021	2.380	-0.658	0.080	0.858	-0.282	-1.315	-0.001
103	A	112	TYR	0	-0.030	-0.027	6.081	-0.060	-0.060	0.000	0.000	0.000	0.000
104	A	113	ILE	0	0.006	0.004	8.983	0.163	0.163	0.000	0.000	0.000	0.000
105	A	114	VAL	0	-0.084	-0.034	4.516	0.233	0.317	-0.001	-0.003	-0.080	0.000
106	A	115	ASP	-1	-0.930	-0.992	7.146	-0.736	-0.736	0.000	0.000	0.000	0.000
107	A	116	GLU	-1	-0.852	-0.920	2.656	-9.650	-6.723	1.632	-1.987	-2.571	-0.024
108	A	117	VAL	0	0.021	-0.001	5.572	-0.612	-0.612	0.000	0.000	0.000	0.000
109	A	118	GLU	-1	-0.917	-0.962	5.217	-3.074	-3.074	0.000	0.000	0.000	0.000
110	A	119	GLU	-1	-0.826	-0.913	3.218	-5.579	-4.172	0.168	-0.513	-1.062	-0.005
111	A	120	ALA	0	-0.046	-0.008	5.640	0.294	0.294	0.000	0.000	0.000	0.000
112	A	121	ILE	0	0.038	0.027	7.916	0.466	0.466	0.000	0.000	0.000	0.000
113	A	122	LYS	1	0.843	0.942	5.307	3.039	3.039	0.000	0.000	0.000	0.000
114	A	123	LEU	0	0.012	0.011	6.585	0.396	0.396	0.000	0.000	0.000	0.000
115	A	124	SER	0	-0.064	-0.077	9.046	0.314	0.314	0.000	0.000	0.000	0.000
116	A	125	ASN	0	0.070	0.035	12.277	0.172	0.172	0.000	0.000	0.000	0.000
117	A	126	VAL	0	-0.042	0.008	10.035	0.151	0.151	0.000	0.000	0.000	0.000
118	A	127	VAL	0	-0.076	-0.057	13.280	0.139	0.139	0.000	0.000	0.000	0.000
119	A	128	LYS	1	1.016	1.005	16.185	0.287	0.287	0.000	0.000	0.000	0.000
120	A	129	TRP	0	0.008	0.003	16.652	0.013	0.013	0.000	0.000	0.000	0.000
121	A	130	GLY	0	0.004	0.006	15.247	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	131	HIS	0	-0.008	-0.031	15.711	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	132	THR	0	0.008	0.007	17.599	0.002	0.002	0.000	0.000	0.000	0.000
124	A	133	PHE	0	-0.008	0.000	13.298	0.009	0.009	0.000	0.000	0.000	0.000
125	A	134	ILE	0	0.000	0.006	12.409	0.008	0.008	0.000	0.000	0.000	0.000
126	A	135	GLU	-1	-0.949	-0.991	16.307	-0.467	-0.467	0.000	0.000	0.000	0.000
127	A	136	LEU	0	-0.057	0.004	19.530	0.042	0.042	0.000	0.000	0.000	0.000
128	A	137	ASN	0	-0.021	-0.023	17.765	0.084	0.084	0.000	0.000	0.000	0.000
129	A	138	LYS	1	1.050	1.042	16.223	0.641	0.641	0.000	0.000	0.000	0.000
130	A	139	GLU	-1	-0.896	-0.963	17.056	-0.444	-0.444	0.000	0.000	0.000	0.000
131	A	140	LEU	0	0.023	0.017	19.106	0.020	0.020	0.000	0.000	0.000	0.000
132	A	141	LEU	0	-0.048	-0.032	13.401	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	142	GLU	-1	-0.878	-0.938	14.526	-0.841	-0.841	0.000	0.000	0.000	0.000
134	A	143	ALA	0	-0.071	-0.032	16.426	0.028	0.028	0.000	0.000	0.000	0.000
135	A	144	TYR	0	-0.056	-0.052	14.734	0.056	0.056	0.000	0.000	0.000	0.000
136	A	145	LYS	1	0.902	0.966	10.984	0.985	0.985	0.000	0.000	0.000	0.000
137	A	146	ASN	0	-0.053	-0.020	12.171	0.153	0.153	0.000	0.000	0.000	0.000
138	A	147	LYS	1	0.915	0.994	13.300	0.517	0.517	0.000	0.000	0.000	0.000
139	A	148	THR	0	0.013	-0.017	15.174	0.002	0.002	0.000	0.000	0.000	0.000
140	A	149	GLU	-1	-0.754	-0.896	16.882	-0.122	-0.122	0.000	0.000	0.000	0.000
141	A	150	GLU	-1	-0.929	-0.967	17.831	-0.109	-0.109	0.000	0.000	0.000	0.000
142	A	151	ASP	-1	-0.862	-0.922	19.691	-0.179	-0.179	0.000	0.000	0.000	0.000
143	A	152	ILE	0	-0.066	-0.027	14.612	-0.022	-0.022	0.000	0.000	0.000	0.000
144	A	153	LYS	1	0.923	0.966	18.994	0.134	0.134	0.000	0.000	0.000	0.000
145	A	154	LYS	1	0.736	0.842	21.388	0.170	0.170	0.000	0.000	0.000	0.000
146	A	155	ILE	0	0.060	0.021	20.497	0.009	0.009	0.000	0.000	0.000	0.000
147	A	156	GLU	-1	-0.764	-0.827	20.744	-0.283	-0.283	0.000	0.000	0.000	0.000
148	A	157	ARG	1	0.877	0.925	22.991	0.162	0.162	0.000	0.000	0.000	0.000
149	A	158	GLU	-1	-0.808	-0.867	26.383	-0.163	-0.163	0.000	0.000	0.000	0.000
150	A	159	ILE	0	-0.038	-0.007	23.047	0.003	0.003	0.000	0.000	0.000	0.000
151	A	160	ILE	0	-0.037	-0.003	25.474	0.012	0.012	0.000	0.000	0.000	0.000

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