FMO DATABASE

FMODB ID: K3RM3

Calculation Name: 5AP8-A-Xray323

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	154
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1557402.406301
FMO2-HF: Nuclear repulsion	1497766.779827
FMO2-HF: Total energy	-59635.626474
FMO2-MP2: Total energy	-59814.805095

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.
-20.416	-9.276	5.264	-5.555	-10.85	-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 : 0.016 / q_NPA : 0.003

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	0.022	0.008	3.530	-1.780	0.108	0.016	-0.880	-1.024	0.002
4	A	4	TYR	0	-0.018	-0.017	5.671	0.293	0.293	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.000	0.000	9.196	-0.131	-0.131	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.018	-0.018	12.323	0.082	0.082	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.915	-0.969	15.597	-0.159	-0.159	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.032	-0.004	18.732	0.037	0.037	0.000	0.000	0.000	0.000
9	A	9	NME	0	0.000	0.001	22.356	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	17	ACE	0	0.098	0.029	19.452	0.010	0.010	0.000	0.000	0.000	0.000
11	A	18	GLY	0	0.002	0.013	15.549	-0.046	-0.046	0.000	0.000	0.000	0.000
12	A	19	LYS	1	0.961	0.978	15.188	0.161	0.161	0.000	0.000	0.000	0.000
13	A	20	LYS	1	0.925	0.981	13.745	0.494	0.494	0.000	0.000	0.000	0.000
14	A	21	LEU	0	0.085	0.022	8.752	0.068	0.068	0.000	0.000	0.000	0.000
15	A	22	VAL	0	0.030	0.039	10.575	0.040	0.040	0.000	0.000	0.000	0.000
16	A	23	LYS	1	0.923	0.968	12.877	0.197	0.197	0.000	0.000	0.000	0.000
17	A	24	LEU	0	-0.075	-0.056	10.926	0.069	0.069	0.000	0.000	0.000	0.000
18	A	25	LYS	1	0.982	0.991	9.713	-0.625	-0.625	0.000	0.000	0.000	0.000
19	A	26	ILE	0	0.003	0.017	5.165	0.230	0.230	0.000	0.000	0.000	0.000
20	A	27	ALA	0	-0.003	0.005	6.298	-0.276	-0.276	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.935	-0.963	8.890	0.678	0.678	0.000	0.000	0.000	0.000
22	A	29	PHE	0	-0.004	-0.012	11.706	-0.075	-0.075	0.000	0.000	0.000	0.000
23	A	30	THR	0	-0.015	-0.022	12.495	0.097	0.097	0.000	0.000	0.000	0.000
24	A	31	ARG	1	0.964	0.979	14.998	-0.122	-0.122	0.000	0.000	0.000	0.000
25	A	32	VAL	0	-0.023	-0.001	15.500	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	33	GLY	0	0.024	0.027	13.170	0.022	0.022	0.000	0.000	0.000	0.000
27	A	34	LYS	1	0.908	0.949	9.772	-0.456	-0.456	0.000	0.000	0.000	0.000
28	A	35	GLY	0	0.023	0.039	7.709	-0.049	-0.049	0.000	0.000	0.000	0.000
29	A	36	VAL	0	0.027	0.011	7.700	-0.077	-0.077	0.000	0.000	0.000	0.000
30	A	37	VAL	0	-0.033	-0.020	8.942	-0.124	-0.124	0.000	0.000	0.000	0.000
31	A	38	LEU	0	0.000	0.000	8.880	0.007	0.007	0.000	0.000	0.000	0.000
32	A	39	ASP	-1	-0.777	-0.895	12.571	-0.090	-0.090	0.000	0.000	0.000	0.000
33	A	40	PRO	0	-0.008	-0.002	16.334	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	41	PHE	0	-0.019	-0.016	19.070	0.012	0.012	0.000	0.000	0.000	0.000
35	A	42	ALA	0	-0.038	0.005	17.742	0.028	0.028	0.000	0.000	0.000	0.000
36	A	43	GLN	0	0.022	-0.006	19.753	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	44	ILE	0	-0.030	-0.002	16.548	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	45	THR	0	-0.030	-0.016	16.260	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	46	LEU	0	-0.045	-0.011	9.027	0.041	0.041	0.000	0.000	0.000	0.000
40	A	47	SER	0	0.022	0.002	12.099	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	48	ASN	0	0.003	0.010	10.864	0.043	0.043	0.000	0.000	0.000	0.000
42	A	49	LYS	1	0.908	0.937	11.936	0.147	0.147	0.000	0.000	0.000	0.000
43	A	50	ASP	-1	-0.791	-0.877	9.415	0.089	0.089	0.000	0.000	0.000	0.000
44	A	51	LYS	1	0.929	0.949	6.924	-0.200	-0.200	0.000	0.000	0.000	0.000
45	A	52	ASP	-1	-0.836	-0.915	6.009	1.351	1.351	0.000	0.000	0.000	0.000
46	A	53	ILE	0	-0.026	-0.003	7.481	0.541	0.541	0.000	0.000	0.000	0.000
47	A	54	VAL	0	0.027	0.019	2.217	-0.268	0.095	1.154	-0.336	-1.180	0.000
48	A	55	ARG	1	0.940	0.981	2.726	-3.317	-0.498	1.384	-1.607	-2.596	-0.008
49	A	56	ARG	1	0.939	0.973	4.085	-0.381	-0.102	0.001	0.212	-0.492	0.000
50	A	57	ILE	0	-0.055	-0.018	5.856	-0.106	-0.106	0.000	0.000	0.000	0.000
51	A	58	GLY	0	0.021	0.013	3.145	-0.138	0.086	0.041	-0.096	-0.169	0.001
52	A	59	ILE	0	0.019	0.016	3.779	-0.679	-0.303	0.003	-0.035	-0.344	0.000
53	A	60	THR	0	-0.003	-0.023	5.893	-0.054	-0.054	0.000	0.000	0.000	0.000
54	A	61	ILE	0	-0.020	-0.020	9.004	-0.057	-0.057	0.000	0.000	0.000	0.000
55	A	62	VAL	0	0.036	0.024	11.471	0.072	0.072	0.000	0.000	0.000	0.000
56	A	63	ASH	0	-0.108	-0.068	15.245	-0.035	-0.035	0.000	0.000	0.000	0.000
57	A	64	THR	0	0.025	0.019	16.864	0.034	0.034	0.000	0.000	0.000	0.000
58	A	65	SER	0	-0.021	-0.013	19.123	-0.046	-0.046	0.000	0.000	0.000	0.000
59	A	66	TRP	0	0.054	0.015	19.930	0.011	0.011	0.000	0.000	0.000	0.000
60	A	67	ASN	0	-0.033	-0.027	22.393	0.008	0.008	0.000	0.000	0.000	0.000
61	A	68	ASN	0	0.018	0.002	25.163	0.007	0.007	0.000	0.000	0.000	0.000
62	A	69	THR	0	0.007	0.032	21.621	0.017	0.017	0.000	0.000	0.000	0.000
63	A	70	SER	0	0.042	0.013	23.914	0.013	0.013	0.000	0.000	0.000	0.000
64	A	71	GLN	0	0.052	0.015	23.018	0.001	0.001	0.000	0.000	0.000	0.000
65	A	72	SER	0	-0.069	-0.047	23.681	0.016	0.016	0.000	0.000	0.000	0.000
66	A	73	GLU	-1	-0.814	-0.894	21.203	-0.115	-0.115	0.000	0.000	0.000	0.000
67	A	74	PHE	0	-0.004	-0.008	15.971	0.001	0.001	0.000	0.000	0.000	0.000
68	A	75	LYS	1	0.909	0.965	19.595	0.010	0.010	0.000	0.000	0.000	0.000
69	A	76	ASN	0	-0.020	-0.013	21.592	0.010	0.010	0.000	0.000	0.000	0.000
70	A	77	ILE	0	-0.001	0.021	15.277	0.027	0.027	0.000	0.000	0.000	0.000
71	A	78	ARG	1	0.973	0.995	16.105	-0.343	-0.343	0.000	0.000	0.000	0.000
72	A	79	GLY	0	0.040	0.015	13.303	0.009	0.009	0.000	0.000	0.000	0.000
73	A	80	GLU	-1	-0.911	-0.956	12.191	0.252	0.252	0.000	0.000	0.000	0.000
74	A	81	HIS	1	0.745	0.843	12.889	-0.055	-0.055	0.000	0.000	0.000	0.000
75	A	82	ARG	1	0.843	0.906	11.904	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	83	ARG	1	0.844	0.922	14.408	0.196	0.196	0.000	0.000	0.000	0.000
77	A	84	ILE	0	-0.017	-0.027	12.423	-0.026	-0.026	0.000	0.000	0.000	0.000
78	A	85	PRO	0	-0.001	0.015	14.613	0.039	0.039	0.000	0.000	0.000	0.000
79	A	86	ILE	0	0.004	0.015	17.773	-0.044	-0.044	0.000	0.000	0.000	0.000
80	A	87	LEU	0	0.022	0.013	15.061	-0.050	-0.050	0.000	0.000	0.000	0.000
81	A	88	PHE	0	0.012	0.004	19.422	0.042	0.042	0.000	0.000	0.000	0.000
82	A	89	ALA	0	0.022	0.019	19.475	-0.056	-0.056	0.000	0.000	0.000	0.000
83	A	90	GLY	0	0.053	0.011	19.304	0.033	0.033	0.000	0.000	0.000	0.000
84	A	91	ASN	0	-0.041	-0.019	19.550	0.050	0.050	0.000	0.000	0.000	0.000
85	A	92	PRO	0	-0.016	-0.029	21.450	0.023	0.023	0.000	0.000	0.000	0.000
86	A	93	ILE	0	-0.043	-0.016	24.038	0.027	0.027	0.000	0.000	0.000	0.000
87	A	94	HIS	0	-0.005	-0.018	22.820	0.029	0.029	0.000	0.000	0.000	0.000
88	A	95	TYR	0	0.014	0.014	23.925	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	96	GLY	0	0.024	0.017	24.065	0.029	0.029	0.000	0.000	0.000	0.000
90	A	97	ILE	0	-0.026	-0.009	25.165	0.013	0.013	0.000	0.000	0.000	0.000
91	A	98	ALA	0	0.056	0.026	23.108	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	99	TYR	0	-0.038	-0.044	20.096	0.027	0.027	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.841	0.934	19.785	0.222	0.222	0.000	0.000	0.000	0.000
94	A	101	LEU	0	-0.030	-0.008	15.291	-0.016	-0.016	0.000	0.000	0.000	0.000
95	A	102	SER	0	-0.027	-0.047	16.449	0.010	0.010	0.000	0.000	0.000	0.000
96	A	103	SER	0	0.027	-0.008	12.659	-0.081	-0.081	0.000	0.000	0.000	0.000
97	A	104	ILE	0	0.005	-0.003	10.457	-0.109	-0.109	0.000	0.000	0.000	0.000
98	A	105	GLU	-1	-0.737	-0.828	11.282	-0.785	-0.785	0.000	0.000	0.000	0.000
99	A	106	ALA	0	0.057	0.038	12.075	-0.087	-0.087	0.000	0.000	0.000	0.000
100	A	107	LEU	0	-0.016	0.001	5.592	-0.073	-0.073	0.000	0.000	0.000	0.000
101	A	108	ILE	0	-0.017	0.000	7.431	-0.422	-0.422	0.000	0.000	0.000	0.000
102	A	109	ALA	0	0.029	0.013	9.335	-0.136	-0.136	0.000	0.000	0.000	0.000
103	A	110	THR	0	-0.018	-0.034	6.166	0.139	0.139	0.000	0.000	0.000	0.000
104	A	111	LEU	0	-0.020	-0.022	2.379	-0.668	0.067	0.863	-0.284	-1.314	-0.001
105	A	112	TYR	0	-0.030	-0.027	6.081	-0.061	-0.061	0.000	0.000	0.000	0.000
106	A	113	ILE	0	0.012	0.006	8.983	0.169	0.169	0.000	0.000	0.000	0.000
107	A	114	VAL	0	-0.087	-0.035	4.515	0.235	0.318	0.000	-0.004	-0.080	0.000
108	A	115	ASP	-1	-0.930	-0.992	7.146	-0.789	-0.789	0.000	0.000	0.000	0.000
109	A	116	GLU	-1	-0.853	-0.921	2.656	-9.955	-7.006	1.633	-2.009	-2.574	-0.024
110	A	117	VAL	0	0.023	-0.001	5.572	-0.601	-0.601	0.000	0.000	0.000	0.000
111	A	118	GLU	-1	-0.912	-0.959	5.217	-3.150	-3.150	0.000	0.000	0.000	0.000
112	A	119	GLU	-1	-0.826	-0.914	3.218	-5.627	-4.203	0.169	-0.516	-1.077	-0.005
113	A	120	ALA	0	-0.048	-0.009	5.640	0.331	0.331	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.039	0.027	7.916	0.486	0.486	0.000	0.000	0.000	0.000
115	A	122	LYS	1	0.845	0.944	5.308	3.080	3.080	0.000	0.000	0.000	0.000
116	A	123	LEU	0	0.012	0.010	6.585	0.405	0.405	0.000	0.000	0.000	0.000
117	A	124	SER	0	-0.069	-0.079	9.046	0.327	0.327	0.000	0.000	0.000	0.000
118	A	125	ASN	0	0.078	0.040	12.277	0.177	0.177	0.000	0.000	0.000	0.000
119	A	126	VAL	0	-0.047	0.005	10.035	0.154	0.154	0.000	0.000	0.000	0.000
120	A	127	VAL	0	-0.080	-0.059	13.281	0.142	0.142	0.000	0.000	0.000	0.000
121	A	128	LYS	1	1.022	1.007	16.185	0.283	0.283	0.000	0.000	0.000	0.000
122	A	129	TRP	0	0.010	0.003	16.652	0.011	0.011	0.000	0.000	0.000	0.000
123	A	130	GLY	0	-0.002	0.002	15.247	-0.010	-0.010	0.000	0.000	0.000	0.000
124	A	131	HIS	0	-0.004	-0.028	15.711	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	132	THR	0	0.008	0.007	17.599	0.003	0.003	0.000	0.000	0.000	0.000
126	A	133	PHE	0	-0.006	-0.002	13.298	0.007	0.007	0.000	0.000	0.000	0.000
127	A	134	ILE	0	-0.002	0.006	12.409	0.005	0.005	0.000	0.000	0.000	0.000
128	A	135	GLU	-1	-0.945	-0.989	16.307	-0.469	-0.469	0.000	0.000	0.000	0.000
129	A	136	LEU	0	-0.052	0.006	19.530	0.044	0.044	0.000	0.000	0.000	0.000
130	A	137	ASN	0	-0.024	-0.025	17.765	0.083	0.083	0.000	0.000	0.000	0.000
131	A	138	LYS	1	1.044	1.040	16.223	0.646	0.646	0.000	0.000	0.000	0.000
132	A	139	GLU	-1	-0.892	-0.961	17.056	-0.451	-0.451	0.000	0.000	0.000	0.000
133	A	140	LEU	0	0.025	0.019	19.106	0.019	0.019	0.000	0.000	0.000	0.000
134	A	141	LEU	0	-0.050	-0.034	13.401	-0.022	-0.022	0.000	0.000	0.000	0.000
135	A	142	GLU	-1	-0.876	-0.938	14.526	-0.857	-0.857	0.000	0.000	0.000	0.000
136	A	143	ALA	0	-0.070	-0.031	16.426	0.029	0.029	0.000	0.000	0.000	0.000
137	A	144	TYR	0	-0.051	-0.050	14.734	0.054	0.054	0.000	0.000	0.000	0.000
138	A	145	LYS	1	0.895	0.963	10.984	1.003	1.003	0.000	0.000	0.000	0.000
139	A	146	ASN	0	-0.052	-0.020	12.171	0.156	0.156	0.000	0.000	0.000	0.000
140	A	147	LYS	1	0.918	0.995	13.300	0.534	0.534	0.000	0.000	0.000	0.000
141	A	148	THR	0	0.014	-0.018	15.174	0.003	0.003	0.000	0.000	0.000	0.000
142	A	149	GLU	-1	-0.755	-0.897	16.882	-0.127	-0.127	0.000	0.000	0.000	0.000
143	A	150	GLU	-1	-0.928	-0.965	17.831	-0.115	-0.115	0.000	0.000	0.000	0.000
144	A	151	ASP	-1	-0.860	-0.920	19.692	-0.187	-0.187	0.000	0.000	0.000	0.000
145	A	152	ILE	0	-0.069	-0.029	14.612	-0.023	-0.023	0.000	0.000	0.000	0.000
146	A	153	LYS	1	0.918	0.962	18.994	0.139	0.139	0.000	0.000	0.000	0.000
147	A	154	LYS	1	0.741	0.845	21.388	0.172	0.172	0.000	0.000	0.000	0.000
148	A	155	ILE	0	0.064	0.024	20.497	0.008	0.008	0.000	0.000	0.000	0.000
149	A	156	GLU	-1	-0.768	-0.828	20.744	-0.285	-0.285	0.000	0.000	0.000	0.000
150	A	157	ARG	1	0.874	0.923	22.991	0.167	0.167	0.000	0.000	0.000	0.000
151	A	158	GLU	-1	-0.801	-0.866	26.393	-0.166	-0.166	0.000	0.000	0.000	0.000
152	A	159	ILE	0	-0.032	-0.009	23.047	0.002	0.002	0.000	0.000	0.000	0.000
153	A	160	ILE	0	-0.075	-0.022	25.480	0.007	0.007	0.000	0.000	0.000	0.000
154	A	161	NME	0	0.031	0.022	28.690	0.007	0.007	0.000	0.000	0.000	0.000

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