FMO DATABASE

FMODB ID: GNRY1

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	OptHSide
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	-1339892.641593
FMO2-HF: Nuclear repulsion	1280666.475608
FMO2-HF: Total energy	-59226.165985
FMO2-MP2: Total energy	-59400.899697

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.
-252.753	-251.988	32.993	-18.343	-15.414	-0.176

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 : 0.906 / q_NPA : 0.912

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	0.035	-0.002	2.844	-0.761	1.740	0.167	-1.134	-1.534	0.001
4	A	5	GLU	-1	-0.723	-0.840	1.686	-155.897	-158.080	32.823	-17.131	-13.509	-0.177
5	A	6	LYS	1	1.004	1.021	3.827	32.351	32.754	0.004	-0.074	-0.332	0.000
6	A	7	LYS	1	0.885	0.947	5.747	27.802	27.802	0.000	0.000	0.000	0.000
7	A	8	GLH	0	-0.050	-0.062	6.829	3.359	3.359	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.060	0.051	7.511	2.075	2.075	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.072	-0.054	9.244	2.901	2.901	0.000	0.000	0.000	0.000
10	A	11	HIS	0	-0.088	-0.032	11.313	1.939	1.939	0.000	0.000	0.000	0.000
11	A	12	PHE	0	0.019	0.000	10.281	1.321	1.321	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.863	0.913	13.360	19.574	19.574	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.006	0.012	15.261	1.142	1.142	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.907	0.963	16.325	17.961	17.961	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.027	0.026	18.118	0.871	0.871	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.840	-0.922	18.923	-15.545	-15.545	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.063	-0.046	21.251	0.821	0.821	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.003	0.000	22.756	0.490	0.490	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.034	-0.001	22.352	0.532	0.532	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.039	-0.029	24.606	0.706	0.706	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.962	-0.967	27.219	-10.830	-10.830	0.000	0.000	0.000	0.000
22	A	23	HIS	1	0.821	0.895	27.514	11.058	11.058	0.000	0.000	0.000	0.000
23	A	24	PHE	0	-0.010	0.015	27.614	0.225	0.225	0.000	0.000	0.000	0.000
24	A	25	PRO	0	0.074	0.055	28.631	-0.329	-0.329	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.841	-0.917	29.818	-10.266	-10.266	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.073	-0.040	26.299	-0.189	-0.189	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.042	-0.020	25.132	-0.593	-0.593	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.036	0.024	24.563	-0.344	-0.344	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.054	-0.026	23.499	-0.580	-0.580	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.088	0.030	18.150	-0.932	-0.932	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.040	-0.014	19.060	-0.908	-0.908	0.000	0.000	0.000	0.000
32	A	33	PHE	0	0.052	0.035	19.012	-0.797	-0.797	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.047	0.034	17.236	-0.868	-0.868	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.082	-0.041	13.870	-1.146	-1.146	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.022	0.019	14.110	-1.607	-1.607	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.861	0.932	14.983	15.207	15.207	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.036	-0.055	13.105	-0.465	-0.465	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.937	-0.974	10.465	-30.552	-30.552	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.883	-0.934	10.504	-21.039	-21.039	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.015	0.009	12.663	-0.445	-0.445	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.030	-0.020	5.666	-1.279	-1.279	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.015	-0.005	8.230	-3.992	-3.992	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.052	0.039	9.227	-0.149	-0.149	0.000	0.000	0.000	0.000
44	A	45	TYR	0	-0.053	-0.053	6.605	-0.436	-0.436	0.000	0.000	0.000	0.000
45	A	46	CYS	0	-0.089	-0.064	5.884	-3.044	-3.000	-0.001	-0.004	-0.039	0.000
46	A	47	ASP	-1	-0.905	-0.946	7.959	-28.542	-28.542	0.000	0.000	0.000	0.000
47	A	48	ALA	0	0.004	-0.006	10.693	1.599	1.599	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.023	-0.025	8.229	1.162	1.162	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.072	-0.031	9.111	1.221	1.221	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.049	-0.023	11.101	2.734	2.734	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.040	-0.007	14.200	1.590	1.590	0.000	0.000	0.000	0.000
52	A	53	PHE	0	-0.036	0.005	14.888	1.220	1.220	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.047	-0.064	13.861	-1.130	-1.130	0.000	0.000	0.000	0.000
54	A	55	HIS	0	0.031	0.020	10.552	-1.819	-1.819	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.008	-0.015	12.653	-0.429	-0.429	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.812	-0.857	15.864	-15.585	-15.585	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.029	0.021	11.949	0.152	0.152	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.816	-0.897	12.420	-20.777	-20.777	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.005	0.026	14.219	0.525	0.525	0.000	0.000	0.000	0.000
60	A	61	MET	0	0.013	0.008	15.926	0.130	0.130	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.004	-0.003	13.551	0.123	0.123	0.000	0.000	0.000	0.000
62	A	63	SER	0	-0.059	-0.059	15.475	0.148	0.148	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.909	-0.940	18.049	-13.293	-13.293	0.000	0.000	0.000	0.000
64	A	65	VAL	0	-0.028	-0.015	15.543	0.431	0.431	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.074	-0.042	15.849	0.208	0.208	0.000	0.000	0.000	0.000
66	A	67	TYR	0	0.017	-0.004	18.403	0.120	0.120	0.000	0.000	0.000	0.000
67	A	68	GLN	0	-0.006	0.020	21.397	0.520	0.520	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.035	-0.025	23.139	-0.251	-0.251	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.095	-0.034	22.983	0.252	0.252	0.000	0.000	0.000	0.000
70	A	71	HIS	0	-0.002	0.000	24.880	0.068	0.068	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.030	0.036	28.990	0.329	0.329	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.018	-0.004	31.489	-0.079	-0.079	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.873	0.919	33.050	9.794	9.794	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.005	-0.002	33.559	0.380	0.380	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.725	-0.863	32.639	-9.630	-9.630	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.010	-0.005	35.950	0.278	0.278	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.070	-0.040	38.870	0.273	0.273	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.007	0.001	37.495	0.229	0.229	0.000	0.000	0.000	0.000
79	A	80	SER	0	0.057	0.032	39.724	0.265	0.265	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.009	0.009	41.481	0.190	0.190	0.000	0.000	0.000	0.000
81	A	82	LEU	0	-0.052	-0.037	42.830	0.194	0.194	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.949	-0.982	40.950	-7.696	-7.696	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.860	0.932	41.522	7.668	7.668	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.877	-0.898	46.848	-6.486	-6.486	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.043	-0.015	48.120	0.118	0.118	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.955	-0.962	48.548	-6.298	-6.298	0.000	0.000	0.000	0.000
87	A	88	GLN	0	-0.016	-0.023	49.860	0.111	0.111	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.925	-0.968	52.756	-5.992	-5.992	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.086	-0.053	48.204	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	91	PRO	0	0.061	0.056	47.873	-0.164	-0.164	0.000	0.000	0.000	0.000
91	A	92	SER	0	0.001	0.007	42.772	-0.057	-0.057	0.000	0.000	0.000	0.000
92	A	93	PRO	0	-0.069	-0.053	42.073	0.173	0.173	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.074	-0.040	42.716	-0.173	-0.173	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.091	0.058	41.947	-0.094	-0.094	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.821	-0.923	38.164	-8.018	-8.018	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.896	0.939	39.001	7.168	7.168	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.030	0.011	41.377	-0.050	-0.050	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.032	0.041	38.994	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	100	PRO	0	0.028	0.005	36.537	-0.073	-0.073	0.000	0.000	0.000	0.000
100	A	101	ILE	0	-0.077	-0.039	38.198	-0.046	-0.046	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.030	0.010	41.436	0.069	0.069	0.000	0.000	0.000	0.000
102	A	103	LEU	0	0.035	0.034	34.970	0.057	0.057	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.878	0.937	37.833	7.936	7.936	0.000	0.000	0.000	0.000
104	A	105	ASN	0	0.005	0.019	40.538	0.155	0.155	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.895	0.933	41.711	7.620	7.620	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.063	0.037	45.372	-0.037	-0.037	0.000	0.000	0.000	0.000
107	A	108	ILE	0	0.073	0.050	41.887	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.039	-0.037	39.188	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.099	-0.050	41.889	-0.063	-0.063	0.000	0.000	0.000	0.000
110	A	111	VAL	0	0.025	0.022	44.022	0.022	0.022	0.000	0.000	0.000	0.000
111	A	112	PHE	0	0.057	0.002	38.882	-0.058	-0.058	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.064	-0.031	39.595	-0.133	-0.133	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.771	0.876	40.678	6.904	6.904	0.000	0.000	0.000	0.000
114	A	115	TYR	0	-0.058	-0.036	39.931	0.109	0.109	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.919	-0.951	34.995	-9.447	-9.447	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.065	-0.027	34.397	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	118	THR	0	0.021	0.000	31.785	-0.319	-0.319	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.784	-0.907	27.195	-11.895	-11.895	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.899	-0.938	30.603	-9.758	-9.758	0.000	0.000	0.000	0.000
120	A	121	PHE	0	0.007	-0.005	33.559	0.383	0.383	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.897	-0.943	35.579	-8.535	-8.535	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.047	-0.021	36.707	0.206	0.206	0.000	0.000	0.000	0.000
123	A	124	SER	0	-0.043	-0.044	38.362	0.142	0.142	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.036	-0.020	40.073	0.139	0.139	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.861	-0.910	41.044	-7.592	-7.592	0.000	0.000	0.000	0.000
126	A	127	TYR	0	-0.063	-0.031	39.208	0.093	0.093	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.857	-0.936	42.031	-7.278	-7.278	0.000	0.000	0.000	0.000
128	A	129	HIS	0	-0.049	-0.024	45.569	0.059	0.059	0.000	0.000	0.000	0.000
129	A	130	LEU	0	0.025	0.024	39.964	0.100	0.100	0.000	0.000	0.000	0.000
130	A	131	TYR	0	-0.043	-0.059	43.106	0.008	0.008	0.000	0.000	0.000	0.000
131	A	132	THR	0	-0.016	-0.013	45.062	0.154	0.154	0.000	0.000	0.000	0.000
132	A	133	GLU	-1	-0.836	-0.875	46.753	-6.744	-6.744	0.000	0.000	0.000	0.000
133	A	134	LEU	0	-0.028	-0.024	41.876	0.088	0.088	0.000	0.000	0.000	0.000
134	A	135	THR	0	0.045	0.012	46.550	0.057	0.057	0.000	0.000	0.000	0.000
135	A	136	GLY	0	0.010	0.006	49.154	0.116	0.116	0.000	0.000	0.000	0.000
136	A	137	THR	0	-0.044	-0.035	47.933	0.113	0.113	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.013	-0.009	45.477	0.062	0.062	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.021	0.020	49.971	0.080	0.080	0.000	0.000	0.000	0.000
139	A	140	LEU	0	0.014	0.022	53.248	0.103	0.103	0.000	0.000	0.000	0.000
140	A	141	LEU	0	-0.057	-0.012	48.256	0.071	0.071	0.000	0.000	0.000	0.000
141	A	142	ILE	0	-0.003	-0.003	51.384	0.067	0.067	0.000	0.000	0.000	0.000
142	A	143	GLU	-1	-0.929	-0.958	54.402	-5.482	-5.482	0.000	0.000	0.000	0.000
143	A	144	SER	0	-0.103	-0.072	55.440	0.085	0.085	0.000	0.000	0.000	0.000
144	A	145	ASN	0	-0.059	-0.022	56.168	0.013	0.013	0.000	0.000	0.000	0.000
145	A	146	HIS	0	-0.084	-0.060	52.776	-0.020	-0.020	0.000	0.000	0.000	0.000
146	A	147	LEU	0	0.015	0.024	48.473	-0.153	-0.153	0.000	0.000	0.000	0.000
147	A	148	PRO	0	-0.041	-0.020	46.073	0.034	0.034	0.000	0.000	0.000	0.000
148	A	149	THR	0	0.043	0.022	48.260	-0.042	-0.042	0.000	0.000	0.000	0.000
149	A	150	ILE	0	-0.054	-0.025	45.030	-0.249	-0.249	0.000	0.000	0.000	0.000

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