FMO DATABASE

FMODB ID: 14Y6Z

Calculation Name: 2APL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2APL

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MW33

Base Structure: X-ray

Registration Date: 2023-03-13

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1339762.946663
FMO2-HF: Nuclear repulsion	1280537.505368
FMO2-HF: Total energy	-59225.441295
FMO2-MP2: Total energy	-59400.206205

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-255.539	-253.143	28.642	-17.629	-13.409	-0.154

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.902 / q_NPA : 0.916

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	4	THR	0	0.037	0.004	3.396	-0.361	2.211	0.117	-1.253	-1.436	0.007
4	A	5	GLU	-1	-0.728	-0.848	1.650	-154.131	-154.697	28.523	-16.324	-11.634	-0.161
5	A	6	LYS	1	0.987	1.012	3.824	30.954	31.281	0.003	-0.044	-0.286	0.000
6	A	7	LYS	1	0.913	0.954	5.735	26.052	26.052	0.000	0.000	0.000	0.000
7	A	8	GLH	0	-0.076	-0.078	7.153	2.744	2.744	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.060	0.045	7.512	1.933	1.933	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.063	-0.036	9.244	2.863	2.863	0.000	0.000	0.000	0.000
10	A	11	HIS	0	-0.028	0.006	11.318	1.842	1.842	0.000	0.000	0.000	0.000
11	A	12	PHE	0	0.026	0.002	10.470	1.305	1.305	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.894	0.920	13.360	19.464	19.464	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.004	0.006	15.257	1.080	1.080	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.890	0.942	16.803	17.449	17.449	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.012	0.021	18.119	0.837	0.837	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.877	-0.950	18.954	-15.056	-15.056	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.051	-0.030	21.288	0.807	0.807	0.000	0.000	0.000	0.000
18	A	19	TYR	0	0.006	0.022	22.759	0.476	0.476	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.021	-0.010	22.425	0.513	0.513	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.031	-0.024	24.700	0.506	0.506	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-1.012	-1.003	27.219	-10.776	-10.776	0.000	0.000	0.000	0.000
22	A	23	HIS	1	0.852	0.915	27.402	10.979	10.979	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.007	0.014	27.647	0.207	0.207	0.000	0.000	0.000	0.000
24	A	25	PRO	0	0.073	0.056	28.661	-0.335	-0.335	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.905	-0.959	29.845	-10.179	-10.179	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.077	-0.045	26.275	-0.193	-0.193	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.043	-0.014	25.147	-0.552	-0.552	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.040	0.027	24.591	-0.330	-0.330	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.050	-0.028	23.569	-0.586	-0.586	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.073	0.035	18.410	-1.005	-1.005	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.038	-0.016	19.053	-0.902	-0.902	0.000	0.000	0.000	0.000
32	A	33	PHE	0	0.051	0.035	18.993	-0.816	-0.816	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.050	0.034	17.211	-0.879	-0.879	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.056	-0.037	13.773	-1.180	-1.180	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.025	0.016	14.103	-1.543	-1.543	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.906	0.963	14.786	14.804	14.804	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.027	-0.041	13.202	-0.445	-0.445	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.947	-0.972	10.255	-29.984	-29.984	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.954	-0.982	10.301	-21.074	-21.074	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.009	0.010	12.464	-0.462	-0.462	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.029	-0.025	5.347	-1.188	-1.188	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.005	0.005	8.045	-4.177	-4.177	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.044	0.035	9.036	-0.222	-0.222	0.000	0.000	0.000	0.000
44	A	45	TYR	0	-0.063	-0.084	7.271	-0.204	-0.204	0.000	0.000	0.000	0.000
45	A	46	CYS	0	-0.073	-0.055	5.639	-3.044	-2.981	-0.001	-0.008	-0.053	0.000
46	A	47	ASP	-1	-0.907	-0.944	7.826	-29.402	-29.402	0.000	0.000	0.000	0.000
47	A	48	ALA	0	0.010	-0.005	10.324	1.552	1.552	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.020	-0.023	8.367	1.143	1.143	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.075	-0.031	8.534	1.178	1.178	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.045	-0.026	10.425	2.555	2.555	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.046	-0.011	13.730	1.606	1.606	0.000	0.000	0.000	0.000
52	A	53	PHE	0	-0.033	0.009	14.867	1.261	1.261	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.037	-0.026	13.970	-1.130	-1.130	0.000	0.000	0.000	0.000
54	A	55	HIS	0	0.031	0.042	11.505	-1.581	-1.581	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.027	-0.002	13.159	-0.391	-0.391	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.858	-0.912	16.447	-15.534	-15.534	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.041	0.027	12.142	0.189	0.189	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.858	-0.923	13.006	-20.696	-20.696	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.060	-0.003	14.732	0.424	0.424	0.000	0.000	0.000	0.000
60	A	61	MET	0	0.056	0.025	15.777	0.070	0.070	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.000	-0.001	13.385	0.136	0.136	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.052	-0.040	15.295	0.219	0.219	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.903	-0.939	18.206	-13.248	-13.248	0.000	0.000	0.000	0.000
64	A	65	VAL	0	-0.024	-0.008	15.343	0.448	0.448	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.065	-0.039	15.649	0.248	0.248	0.000	0.000	0.000	0.000
66	A	67	TYR	0	0.002	-0.009	18.205	0.201	0.201	0.000	0.000	0.000	0.000
67	A	68	GLN	0	0.042	0.044	21.052	0.671	0.671	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.055	-0.040	22.939	-0.265	-0.265	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.096	-0.040	22.795	0.248	0.248	0.000	0.000	0.000	0.000
70	A	71	HIS	0	-0.005	-0.008	24.548	0.144	0.144	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.042	0.039	28.792	0.338	0.338	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.006	-0.012	31.287	-0.071	-0.071	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.932	0.954	32.850	9.517	9.517	0.000	0.000	0.000	0.000
74	A	75	TYR	0	0.008	0.004	33.784	0.373	0.373	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.712	-0.845	32.745	-9.514	-9.514	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.031	-0.010	35.955	0.281	0.281	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.072	-0.041	38.760	0.265	0.265	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.005	0.007	37.530	0.230	0.230	0.000	0.000	0.000	0.000
79	A	80	SER	0	0.061	0.029	39.832	0.268	0.268	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.012	0.013	41.488	0.182	0.182	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.059	-0.039	42.815	0.191	0.191	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.963	-0.987	41.176	-7.613	-7.613	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.865	0.934	42.368	7.551	7.551	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.869	-0.880	46.856	-6.444	-6.444	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.045	-0.019	48.094	0.115	0.115	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.953	-0.959	48.333	-6.323	-6.323	0.000	0.000	0.000	0.000
87	A	88	GLN	0	-0.028	-0.029	49.863	0.099	0.099	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.925	-0.964	52.693	-5.976	-5.976	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.090	-0.057	48.311	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	91	PRO	0	0.083	0.065	47.873	-0.163	-0.163	0.000	0.000	0.000	0.000
91	A	92	SER	0	0.011	0.011	42.845	-0.060	-0.060	0.000	0.000	0.000	0.000
92	A	93	PRO	0	-0.034	-0.037	42.282	0.159	0.159	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.074	-0.043	42.713	-0.172	-0.172	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.077	0.051	41.994	-0.103	-0.103	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.859	-0.941	37.922	-8.175	-8.175	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.896	0.943	38.996	7.163	7.163	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.032	0.006	41.371	-0.055	-0.055	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.026	0.044	38.869	0.002	0.002	0.000	0.000	0.000	0.000
99	A	100	PRO	0	0.034	0.008	36.605	-0.071	-0.071	0.000	0.000	0.000	0.000
100	A	101	ILE	0	-0.093	-0.039	38.227	-0.048	-0.048	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.033	0.004	41.459	0.069	0.069	0.000	0.000	0.000	0.000
102	A	103	LEU	0	0.027	0.032	34.926	0.063	0.063	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.868	0.926	38.022	7.820	7.820	0.000	0.000	0.000	0.000
104	A	105	ASN	0	0.011	0.025	40.547	0.148	0.148	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.916	0.945	41.778	7.535	7.535	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.047	0.030	45.280	-0.035	-0.035	0.000	0.000	0.000	0.000
107	A	108	ILE	0	0.082	0.047	41.718	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.040	-0.033	38.950	0.033	0.033	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.108	-0.051	41.688	-0.074	-0.074	0.000	0.000	0.000	0.000
110	A	111	VAL	0	0.044	0.033	43.750	0.019	0.019	0.000	0.000	0.000	0.000
111	A	112	PHE	0	0.053	-0.003	38.670	-0.072	-0.072	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.062	-0.031	39.391	-0.133	-0.133	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.770	0.881	40.476	6.819	6.819	0.000	0.000	0.000	0.000
114	A	115	TYR	0	-0.044	-0.026	39.719	0.097	0.097	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.923	-0.954	34.892	-9.382	-9.382	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.073	-0.034	34.183	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	118	THR	0	0.018	0.001	31.578	-0.294	-0.294	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.780	-0.895	26.843	-11.704	-11.704	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.911	-0.953	30.404	-9.806	-9.806	0.000	0.000	0.000	0.000
120	A	121	PHE	0	-0.005	-0.011	33.364	0.369	0.369	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.966	-1.003	35.381	-8.491	-8.491	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.034	-0.010	36.525	0.202	0.202	0.000	0.000	0.000	0.000
123	A	124	SER	0	-0.025	-0.007	38.187	0.131	0.131	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.015	-0.015	39.877	0.123	0.123	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.908	-0.959	40.999	-7.523	-7.523	0.000	0.000	0.000	0.000
126	A	127	TYR	0	0.016	0.033	39.132	0.071	0.071	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.862	-0.949	41.831	-7.335	-7.335	0.000	0.000	0.000	0.000
128	A	129	HIS	0	-0.055	-0.027	45.370	0.065	0.065	0.000	0.000	0.000	0.000
129	A	130	LEU	0	0.027	0.029	39.794	0.102	0.102	0.000	0.000	0.000	0.000
130	A	131	TYR	0	-0.057	-0.079	42.988	0.017	0.017	0.000	0.000	0.000	0.000
131	A	132	THR	0	-0.015	-0.001	44.862	0.155	0.155	0.000	0.000	0.000	0.000
132	A	133	GLU	-1	-0.836	-0.884	46.565	-6.720	-6.720	0.000	0.000	0.000	0.000
133	A	134	LEU	0	-0.031	-0.032	41.641	0.085	0.085	0.000	0.000	0.000	0.000
134	A	135	THR	0	0.041	0.010	46.349	0.056	0.056	0.000	0.000	0.000	0.000
135	A	136	GLY	0	0.011	0.006	48.963	0.115	0.115	0.000	0.000	0.000	0.000
136	A	137	THR	0	-0.037	-0.026	47.686	0.118	0.118	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.011	-0.009	45.440	0.059	0.059	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.032	0.024	49.959	0.080	0.080	0.000	0.000	0.000	0.000
139	A	140	LEU	0	0.008	0.019	53.174	0.103	0.103	0.000	0.000	0.000	0.000
140	A	141	LEU	0	-0.062	-0.026	48.158	0.072	0.072	0.000	0.000	0.000	0.000
141	A	142	ILE	0	-0.002	-0.002	51.594	0.067	0.067	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.943	-0.966	54.434	-5.452	-5.452	0.000	0.000	0.000	0.000
143	A	144	SER	0	-0.113	-0.063	55.372	0.089	0.089	0.000	0.000	0.000	0.000
144	A	145	ASN	0	-0.049	-0.026	56.208	-0.018	-0.018	0.000	0.000	0.000	0.000
145	A	146	HIS	0	-0.071	-0.042	52.770	-0.023	-0.023	0.000	0.000	0.000	0.000
146	A	147	LEU	0	0.008	0.017	48.316	-0.154	-0.154	0.000	0.000	0.000	0.000
147	A	148	PRO	0	-0.032	-0.015	45.988	0.038	0.038	0.000	0.000	0.000	0.000
148	A	149	THR	0	0.028	0.008	48.286	-0.038	-0.038	0.000	0.000	0.000	0.000
149	A	150	ILE	0	-0.034	-0.011	44.257	-0.164	-0.164	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)