FMO DATABASE

FMODB ID: 827NY

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:

Apendix: None

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1343843.985177
FMO2-HF: Nuclear repulsion	1284617.485926
FMO2-HF: Total energy	-59226.499251
FMO2-MP2: Total energy	-59401.12019

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.
-246.981	-245.707	29.709	-17.255	-13.728	-0.177

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 : 0.905 / q_NPA : 0.919

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	0.042	0.004	3.008	-0.899	1.257	0.050	-0.957	-1.249	0.002
4	A	5	GLU	-1	-0.738	-0.839	1.704	-153.977	-155.368	29.660	-16.147	-12.123	-0.179
5	A	6	LYS	1	0.998	1.005	3.923	34.169	34.640	0.000	-0.147	-0.324	0.000
6	A	7	LYS	1	0.887	0.950	5.997	28.209	28.209	0.000	0.000	0.000	0.000
7	A	8	GLH	0	-0.025	-0.039	7.467	3.604	3.604	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.053	0.041	7.396	2.216	2.216	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.064	-0.051	9.475	2.881	2.881	0.000	0.000	0.000	0.000
10	A	11	HIS	0	-0.085	-0.039	11.634	1.937	1.937	0.000	0.000	0.000	0.000
11	A	12	PHE	0	0.030	0.003	10.789	1.296	1.296	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.846	0.918	13.538	19.765	19.765	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.004	0.007	15.300	1.159	1.159	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.862	0.943	16.044	19.078	19.078	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.034	0.040	18.025	0.869	0.869	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.814	-0.913	18.690	-15.699	-15.699	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.064	-0.033	21.220	0.837	0.837	0.000	0.000	0.000	0.000
18	A	19	TYR	0	0.010	-0.003	22.961	0.536	0.536	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.019	-0.003	22.142	0.520	0.520	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.093	-0.071	24.273	0.862	0.862	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.934	-0.945	27.277	-10.977	-10.977	0.000	0.000	0.000	0.000
22	A	23	HIS	1	0.819	0.889	27.791	11.065	11.065	0.000	0.000	0.000	0.000
23	A	24	PHE	0	0.001	0.023	27.439	0.224	0.224	0.000	0.000	0.000	0.000
24	A	25	PRO	0	0.087	0.057	28.489	-0.346	-0.346	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.841	-0.909	29.992	-10.313	-10.313	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.071	-0.041	26.116	-0.227	-0.227	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.041	-0.018	25.231	-0.610	-0.610	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.046	0.028	24.341	-0.405	-0.405	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.029	-0.013	23.400	-0.581	-0.581	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.079	0.029	18.107	-1.060	-1.060	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.041	-0.013	18.700	-0.993	-0.993	0.000	0.000	0.000	0.000
32	A	33	PHE	0	0.046	0.031	18.391	-0.948	-0.948	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.030	0.022	17.420	-0.843	-0.843	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.075	-0.032	13.482	-1.115	-1.115	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.035	0.019	14.087	-1.476	-1.476	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.806	0.897	14.517	15.346	15.346	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.020	-0.036	12.577	-0.257	-0.257	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.922	-0.974	10.002	-31.610	-31.610	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.852	-0.893	10.632	-20.451	-20.451	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.037	0.026	12.695	-0.612	-0.612	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.030	-0.023	5.444	-1.561	-1.561	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.027	-0.022	8.347	-3.954	-3.954	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.041	0.025	9.335	-0.420	-0.420	0.000	0.000	0.000	0.000
44	A	45	TYR	0	-0.056	-0.046	7.008	-0.214	-0.214	0.000	0.000	0.000	0.000
45	A	46	CYS	0	-0.087	-0.062	5.882	-3.428	-3.390	-0.001	-0.004	-0.032	0.000
46	A	47	ASP	-1	-0.854	-0.926	8.093	-26.157	-26.157	0.000	0.000	0.000	0.000
47	A	48	ALA	0	0.008	0.008	10.991	1.499	1.499	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.021	-0.019	8.713	1.173	1.173	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.084	-0.038	9.295	0.964	0.964	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.093	-0.052	11.310	2.812	2.812	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.027	-0.002	14.323	1.571	1.571	0.000	0.000	0.000	0.000
52	A	53	PHE	0	-0.055	-0.010	15.296	1.118	1.118	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.052	-0.065	13.885	-1.270	-1.270	0.000	0.000	0.000	0.000
54	A	55	HIS	0	0.001	0.006	10.373	-1.466	-1.466	0.000	0.000	0.000	0.000
55	A	56	PRO	0	-0.008	-0.023	13.077	-0.372	-0.372	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.790	-0.849	16.522	-15.766	-15.766	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.035	0.021	12.434	0.130	0.130	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.790	-0.879	13.254	-20.532	-20.532	0.000	0.000	0.000	0.000
59	A	60	SER	0	0.022	0.031	14.567	0.585	0.585	0.000	0.000	0.000	0.000
60	A	61	MET	0	0.007	0.005	16.089	0.089	0.089	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.010	-0.003	13.579	0.131	0.131	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.049	-0.058	15.507	-0.037	-0.037	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.905	-0.941	18.427	-13.348	-13.348	0.000	0.000	0.000	0.000
64	A	65	VAL	0	-0.041	-0.023	15.653	0.366	0.366	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.077	-0.042	15.861	0.073	0.073	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.004	-0.024	18.519	0.134	0.134	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.040	-0.007	21.600	0.459	0.459	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.023	-0.018	23.326	-0.397	-0.397	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.071	-0.027	22.974	0.237	0.237	0.000	0.000	0.000	0.000
70	A	71	HIS	0	-0.016	-0.009	24.553	0.029	0.029	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.042	0.039	28.825	0.342	0.342	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.012	-0.010	31.409	-0.064	-0.064	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.868	0.913	32.878	9.926	9.926	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.005	-0.003	33.323	0.406	0.406	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.760	-0.873	32.550	-9.662	-9.662	0.000	0.000	0.000	0.000
76	A	77	THR	0	0.000	-0.005	35.895	0.296	0.296	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.047	-0.028	38.712	0.264	0.264	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.028	-0.012	37.416	0.222	0.222	0.000	0.000	0.000	0.000
79	A	80	SER	0	0.034	0.022	39.538	0.281	0.281	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.018	0.004	41.306	0.180	0.180	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.065	-0.034	42.711	0.197	0.197	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.951	-0.990	40.888	-7.790	-7.790	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.857	0.942	41.409	7.707	7.707	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.874	-0.907	47.128	-6.543	-6.543	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.040	-0.019	47.970	0.120	0.120	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.935	-0.962	49.074	-6.272	-6.272	0.000	0.000	0.000	0.000
87	A	88	GLN	0	-0.020	-0.013	50.042	0.107	0.107	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.929	-0.973	52.612	-6.015	-6.015	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.082	-0.047	47.944	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	91	PRO	0	0.091	0.062	47.524	-0.183	-0.183	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.033	-0.014	42.576	-0.066	-0.066	0.000	0.000	0.000	0.000
92	A	93	PRO	0	-0.069	-0.044	42.270	0.172	0.172	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.052	-0.022	43.248	-0.110	-0.110	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.071	0.042	42.033	-0.115	-0.115	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.769	-0.897	37.907	-7.899	-7.899	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.854	0.917	38.486	7.177	7.177	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.023	0.009	40.814	-0.041	-0.041	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.048	0.047	38.879	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	100	PRO	0	0.022	-0.001	36.131	-0.075	-0.075	0.000	0.000	0.000	0.000
100	A	101	ILE	0	-0.068	-0.031	37.848	-0.051	-0.051	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.032	0.010	41.052	0.084	0.084	0.000	0.000	0.000	0.000
102	A	103	LEU	0	0.014	0.026	34.847	0.073	0.073	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.881	0.937	37.412	7.978	7.978	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.001	0.009	40.492	0.146	0.146	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.892	0.931	41.399	7.655	7.655	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.059	0.048	45.291	-0.054	-0.054	0.000	0.000	0.000	0.000
107	A	108	ILE	0	0.078	0.051	41.660	-0.027	-0.027	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.031	-0.028	38.836	-0.016	-0.016	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.098	-0.060	41.785	-0.048	-0.048	0.000	0.000	0.000	0.000
110	A	111	VAL	0	0.001	0.008	44.027	0.016	0.016	0.000	0.000	0.000	0.000
111	A	112	PHE	0	0.066	0.006	38.617	-0.049	-0.049	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.063	-0.032	39.676	-0.124	-0.124	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.769	0.877	40.753	6.987	6.987	0.000	0.000	0.000	0.000
114	A	115	TYR	0	-0.049	-0.033	39.972	0.149	0.149	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.933	-0.961	34.750	-9.545	-9.545	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.054	-0.015	34.197	0.006	0.006	0.000	0.000	0.000	0.000
117	A	118	THR	0	0.005	-0.024	31.763	-0.321	-0.321	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.789	-0.884	27.065	-12.109	-12.109	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.859	-0.921	30.301	-9.821	-9.821	0.000	0.000	0.000	0.000
120	A	121	PHE	0	0.010	0.013	33.248	0.380	0.380	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.889	-0.929	35.571	-8.522	-8.522	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.058	-0.020	36.684	0.201	0.201	0.000	0.000	0.000	0.000
123	A	124	SER	0	-0.046	-0.040	38.317	0.139	0.139	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.032	-0.028	40.115	0.104	0.104	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.867	-0.915	41.322	-7.652	-7.652	0.000	0.000	0.000	0.000
126	A	127	TYR	0	-0.050	-0.042	39.195	0.073	0.073	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.864	-0.937	41.972	-7.246	-7.246	0.000	0.000	0.000	0.000
128	A	129	HIS	0	-0.060	-0.018	45.527	0.059	0.059	0.000	0.000	0.000	0.000
129	A	130	LEU	0	0.027	0.022	39.887	0.098	0.098	0.000	0.000	0.000	0.000
130	A	131	TYR	0	-0.026	-0.042	42.879	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	132	THR	0	-0.024	-0.019	44.834	0.154	0.154	0.000	0.000	0.000	0.000
132	A	133	GLU	-1	-0.824	-0.872	46.767	-6.781	-6.781	0.000	0.000	0.000	0.000
133	A	134	LEU	0	-0.026	-0.008	41.626	0.085	0.085	0.000	0.000	0.000	0.000
134	A	135	THR	0	0.042	0.009	46.235	0.057	0.057	0.000	0.000	0.000	0.000
135	A	136	GLY	0	0.011	0.002	48.702	0.117	0.117	0.000	0.000	0.000	0.000
136	A	137	THR	0	-0.066	-0.052	47.633	0.113	0.113	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.013	-0.011	45.122	0.053	0.053	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.013	0.019	49.629	0.080	0.080	0.000	0.000	0.000	0.000
139	A	140	LEU	0	0.021	0.019	53.136	0.093	0.093	0.000	0.000	0.000	0.000
140	A	141	LEU	0	-0.056	-0.010	48.223	0.066	0.066	0.000	0.000	0.000	0.000
141	A	142	ILE	0	0.004	0.009	51.397	0.053	0.053	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.924	-0.965	54.353	-5.520	-5.520	0.000	0.000	0.000	0.000
143	A	144	SER	0	-0.089	-0.065	55.264	0.088	0.088	0.000	0.000	0.000	0.000
144	A	145	ASN	0	-0.071	-0.030	55.913	0.053	0.053	0.000	0.000	0.000	0.000
145	A	146	HIS	0	-0.082	-0.060	52.601	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	147	LEU	0	0.011	0.025	48.293	-0.157	-0.157	0.000	0.000	0.000	0.000
147	A	148	PRO	0	-0.047	-0.024	45.766	0.039	0.039	0.000	0.000	0.000	0.000
148	A	149	THR	0	0.052	0.031	47.912	-0.019	-0.019	0.000	0.000	0.000	0.000
149	A	150	ILE	0	-0.058	-0.028	44.647	-0.263	-0.263	0.000	0.000	0.000	0.000

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