FMO DATABASE

FMODB ID: 3NYYL

Calculation Name: 2APL-A-Xray307

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: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	151
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1346516.926167
FMO2-HF: Nuclear repulsion	1287120.591903
FMO2-HF: Total energy	-59396.334264
FMO2-MP2: Total energy	-59571.63959

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:ACE )

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

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.
-3.29	-1.118	0.407	-1.141	-1.437	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.026

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	SER	0	0.002	0.011	3.865	0.423	1.538	-0.005	-0.583	-0.527	-0.001
4	A	4	THR	0	0.029	-0.001	2.627	-0.409	0.019	0.318	-0.290	-0.456	0.001
5	A	5	GLU	-1	-0.758	-0.870	3.081	-3.857	-3.285	0.094	-0.265	-0.401	-0.001
6	A	6	LYS	1	0.993	1.015	5.383	0.500	0.557	0.000	-0.003	-0.053	0.000
7	A	7	LYS	1	0.912	0.954	7.738	-0.167	-0.167	0.000	0.000	0.000	0.000
8	A	8	GLH	0	-0.075	-0.078	7.251	0.087	0.087	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.059	0.045	9.090	0.022	0.022	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.061	-0.035	11.052	0.045	0.045	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.028	0.005	12.362	0.013	0.013	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.022	0.000	10.330	0.016	0.016	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.897	0.921	14.982	0.142	0.142	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.000	0.008	16.990	0.011	0.011	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.888	0.941	16.893	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.013	0.021	19.336	0.005	0.005	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.878	-0.950	20.963	-0.080	-0.080	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.050	-0.029	22.720	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.001	0.021	23.842	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.021	-0.010	24.490	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.026	-0.022	26.667	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-1.013	-1.002	28.049	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	HIS	1	0.850	0.913	28.131	0.010	0.010	0.000	0.000	0.000	0.000
24	A	24	PHE	0	-0.007	0.013	28.870	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.074	0.057	30.674	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.907	-0.958	32.236	-0.034	-0.034	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.072	-0.043	28.750	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.048	-0.015	27.503	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.043	0.028	27.270	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.051	-0.029	27.113	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	31	ASN	0	0.072	0.034	22.625	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.037	-0.015	22.880	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.051	0.035	22.785	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.048	0.034	20.157	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.055	-0.036	18.041	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.025	0.016	17.558	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.908	0.964	18.171	0.059	0.059	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.032	-0.043	15.400	0.010	0.010	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.940	-0.970	13.481	-0.332	-0.332	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.958	-0.983	13.377	-0.145	-0.145	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.013	0.011	14.498	0.010	0.010	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.031	-0.027	7.125	0.016	0.016	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.001	0.007	9.613	-0.038	-0.038	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.042	0.035	11.333	0.030	0.030	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.068	-0.087	5.935	0.144	0.144	0.000	0.000	0.000	0.000
46	A	46	CYS	0	-0.070	-0.054	6.434	0.022	0.022	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.906	-0.943	7.762	-0.060	-0.060	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.011	-0.006	10.920	0.057	0.057	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.031	-0.026	6.370	0.082	0.082	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.067	-0.028	8.205	0.061	0.061	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.046	-0.026	9.321	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.046	-0.011	12.011	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.033	0.008	13.103	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.038	-0.027	12.007	0.081	0.081	0.000	0.000	0.000	0.000
55	A	55	HIS	0	0.030	0.042	9.831	0.059	0.059	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.028	-0.002	11.299	-0.048	-0.048	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.858	-0.912	14.760	0.156	0.156	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.038	0.026	10.759	-0.035	-0.035	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.860	-0.924	11.996	0.129	0.129	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.052	0.000	13.556	-0.043	-0.043	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.056	0.025	15.095	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.001	-0.001	13.058	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.056	-0.041	15.156	-0.026	-0.026	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.900	-0.938	17.854	0.017	0.017	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.021	-0.007	17.033	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.070	-0.041	16.613	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.001	-0.009	19.266	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	GLN	0	0.042	0.044	22.361	0.006	0.006	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.052	-0.039	24.236	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.096	-0.040	24.259	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	71	HIS	0	-0.006	-0.009	24.971	0.007	0.007	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.045	0.040	29.528	0.002	0.002	0.000	0.000	0.000	0.000
73	A	73	SER	0	0.003	-0.014	32.353	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.931	0.954	34.006	0.028	0.028	0.000	0.000	0.000	0.000
75	A	75	TYR	0	0.013	0.006	34.963	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.713	-0.845	33.365	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.032	-0.011	36.779	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.074	-0.042	39.583	0.001	0.001	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.004	0.006	38.638	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	SER	0	0.063	0.031	40.269	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.015	0.014	42.057	0.001	0.001	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.064	-0.040	44.003	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.961	-0.986	41.717	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.866	0.935	42.170	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.871	-0.881	47.244	0.000	0.000	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.044	-0.020	48.961	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.952	-0.957	48.940	0.000	0.000	0.000	0.000	0.000	0.000
88	A	88	GLN	0	-0.029	-0.029	50.593	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.924	-0.964	53.778	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.093	-0.058	49.619	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.085	0.065	48.946	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.008	0.010	43.863	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.033	-0.036	43.650	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.071	-0.040	44.126	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.075	0.049	43.055	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.861	-0.942	39.294	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.904	0.948	40.611	0.009	0.009	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.036	0.006	43.089	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.027	0.044	40.272	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.034	0.008	38.582	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.095	-0.041	40.276	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.034	0.004	43.755	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.024	0.031	36.867	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.871	0.928	40.897	0.023	0.023	0.000	0.000	0.000	0.000
105	A	105	ASN	0	0.012	0.024	43.133	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.914	0.944	44.764	0.024	0.024	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.048	0.031	47.916	0.000	0.000	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.082	0.047	43.691	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	GLN	0	-0.040	-0.034	41.574	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.108	-0.051	44.095	0.000	0.000	0.000	0.000	0.000	0.000
111	A	111	VAL	0	0.045	0.034	45.500	0.000	0.000	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.051	-0.004	40.284	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.062	-0.031	41.807	0.000	0.000	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.771	0.881	42.920	0.011	0.011	0.000	0.000	0.000	0.000
115	A	115	TYR	0	-0.045	-0.027	41.400	0.001	0.001	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.920	-0.953	37.028	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.073	-0.033	36.063	0.001	0.001	0.000	0.000	0.000	0.000
118	A	118	THR	0	0.015	-0.001	33.206	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.781	-0.895	27.943	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.913	-0.954	31.374	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	121	PHE	0	-0.005	-0.010	33.965	0.002	0.002	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.965	-1.003	36.012	0.002	0.002	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.034	-0.010	36.602	0.001	0.001	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.026	-0.007	38.351	0.000	0.000	0.000	0.000	0.000	0.000
125	A	125	PRO	0	-0.015	-0.015	40.462	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.908	-0.959	42.148	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	TYR	0	0.017	0.033	39.909	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.861	-0.948	42.623	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	HIS	0	-0.054	-0.027	45.992	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.025	0.028	41.152	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.058	-0.079	43.544	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	THR	0	-0.015	-0.001	45.747	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.836	-0.884	48.036	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.029	-0.032	42.994	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	135	THR	0	0.033	0.007	47.689	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	GLY	0	0.019	0.009	49.993	0.000	0.000	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.037	-0.026	49.561	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	138	ILE	0	-0.017	-0.011	46.708	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.037	0.025	51.349	0.000	0.000	0.000	0.000	0.000	0.000
140	A	140	LEU	0	0.008	0.019	54.658	0.000	0.000	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.065	-0.027	50.052	0.000	0.000	0.000	0.000	0.000	0.000
142	A	142	ILE	0	-0.003	-0.002	52.819	0.000	0.000	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.941	-0.965	56.010	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	144	SER	0	-0.115	-0.064	57.270	0.000	0.000	0.000	0.000	0.000	0.000
145	A	145	ASN	0	-0.048	-0.025	58.153	0.000	0.000	0.000	0.000	0.000	0.000
146	A	146	HIS	0	-0.070	-0.042	55.069	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	147	LEU	0	0.008	0.017	49.976	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	148	PRO	0	-0.028	-0.013	48.173	0.000	0.000	0.000	0.000	0.000	0.000
149	A	149	THR	0	0.048	0.013	50.416	0.000	0.000	0.000	0.000	0.000	0.000
150	A	150	ILE	0	-0.065	-0.025	48.068	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	151	NME	0	-0.006	0.002	45.237	0.001	0.001	0.000	0.000	0.000	0.000

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