FMO DATABASE

FMODB ID: R8Y98

Calculation Name: 1AF5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AF5

Chain ID: A

ChEMBL ID:

UniProt ID: P05725

Base Structure: X-ray

Registration Date: 2023-09-22

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1100392.94615
FMO2-HF: Nuclear repulsion	1050621.693981
FMO2-HF: Total energy	-49771.252168
FMO2-MP2: Total energy	-49920.772318

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:4:LYS)

Summations of interaction energy for fragment #1(A:4: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.
-35.015	-29.056	20.14	-10.744	-15.356	-0.112

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.926 / q_NPA : 0.977

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

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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	6	ASN	0	-0.005	-0.011	1.759	-36.246	-37.216	11.860	-5.516	-5.373	-0.050
4	A	7	LYS	1	0.932	0.950	5.073	46.332	46.468	-0.001	-0.009	-0.127	0.000
5	A	8	GLU	-1	-0.865	-0.909	7.804	-22.839	-22.839	0.000	0.000	0.000	0.000
6	A	9	PHE	0	0.042	0.003	3.943	1.124	1.344	-0.001	-0.020	-0.199	0.000
7	A	10	LEU	0	-0.064	-0.015	3.364	-1.348	-1.048	0.016	-0.063	-0.253	0.000
8	A	11	LEU	0	0.032	0.023	6.865	1.726	1.726	0.000	0.000	0.000	0.000
9	A	12	TYR	0	-0.013	-0.009	9.710	2.355	2.355	0.000	0.000	0.000	0.000
10	A	13	LEU	0	-0.024	-0.015	4.868	1.360	1.360	0.000	0.000	0.000	0.000
11	A	14	ALA	0	0.068	0.034	8.736	0.772	0.772	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.019	0.023	10.547	1.978	1.978	0.000	0.000	0.000	0.000
13	A	16	PHE	0	0.007	-0.014	11.538	1.093	1.093	0.000	0.000	0.000	0.000
14	A	17	VAL	0	0.005	0.019	9.236	1.035	1.035	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.729	-0.869	12.303	-17.974	-17.974	0.000	0.000	0.000	0.000
16	A	19	GLY	0	-0.037	-0.006	15.090	1.496	1.496	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.952	-0.985	15.495	-16.728	-16.728	0.000	0.000	0.000	0.000
18	A	21	GLY	0	0.076	0.003	13.058	-1.457	-1.457	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.094	-0.025	13.854	1.272	1.272	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.012	-0.003	11.797	-1.665	-1.665	0.000	0.000	0.000	0.000
21	A	24	ILE	0	0.024	0.014	13.955	0.955	0.955	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.055	0.024	16.137	-1.030	-1.030	0.000	0.000	0.000	0.000
23	A	26	GLN	0	-0.020	-0.017	18.455	0.670	0.670	0.000	0.000	0.000	0.000
24	A	27	ILE	0	0.062	0.031	21.539	-0.488	-0.488	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.913	0.945	19.640	15.497	15.497	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.024	-0.001	25.452	0.104	0.104	0.000	0.000	0.000	0.000
27	A	30	ASN	0	0.058	0.001	26.852	0.002	0.002	0.000	0.000	0.000	0.000
28	A	31	GLN	0	0.024	0.003	29.085	0.511	0.511	0.000	0.000	0.000	0.000
29	A	32	SER	0	0.008	-0.022	32.070	0.341	0.341	0.000	0.000	0.000	0.000
30	A	33	TYR	0	0.011	0.010	32.573	-0.210	-0.210	0.000	0.000	0.000	0.000
31	A	34	LYS	1	1.022	1.016	32.599	8.860	8.860	0.000	0.000	0.000	0.000
32	A	35	PHE	0	0.009	0.015	32.657	-0.264	-0.264	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.804	0.910	30.991	9.315	9.315	0.000	0.000	0.000	0.000
34	A	37	HIS	0	0.053	0.025	28.170	-0.138	-0.138	0.000	0.000	0.000	0.000
35	A	38	GLN	0	-0.001	-0.005	20.741	0.092	0.092	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.014	0.044	20.006	0.129	0.129	0.000	0.000	0.000	0.000
37	A	40	SER	0	-0.028	-0.006	17.960	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	41	LEU	0	-0.005	0.012	14.451	0.394	0.394	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.043	-0.041	13.140	-0.769	-0.769	0.000	0.000	0.000	0.000
40	A	43	PHE	0	0.029	0.021	7.459	0.123	0.123	0.000	0.000	0.000	0.000
41	A	44	GLN	0	-0.009	-0.022	11.491	0.373	0.373	0.000	0.000	0.000	0.000
42	A	45	VAL	0	0.033	0.018	10.985	-0.265	-0.265	0.000	0.000	0.000	0.000
43	A	46	THR	0	-0.043	-0.023	13.734	0.334	0.334	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.073	0.051	16.274	1.087	1.087	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.974	0.975	18.685	12.364	12.364	0.000	0.000	0.000	0.000
46	A	49	THR	0	0.061	0.018	20.909	-0.756	-0.756	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.038	-0.013	22.163	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	51	ARG	1	0.878	0.935	18.953	15.362	15.362	0.000	0.000	0.000	0.000
49	A	52	ARG	1	1.061	1.033	15.446	16.780	16.780	0.000	0.000	0.000	0.000
50	A	53	TRP	0	0.071	0.027	15.634	-1.452	-1.452	0.000	0.000	0.000	0.000
51	A	54	PHE	0	0.041	0.025	12.338	-0.973	-0.973	0.000	0.000	0.000	0.000
52	A	55	LEU	0	-0.005	0.002	12.366	-1.721	-1.721	0.000	0.000	0.000	0.000
53	A	56	GLY	0	-0.059	-0.034	11.638	-1.231	-1.231	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.909	0.955	10.455	24.871	24.871	0.000	0.000	0.000	0.000
55	A	58	LEU	0	-0.010	0.003	8.317	-2.589	-2.589	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.012	-0.014	6.492	-5.729	-5.729	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.897	-0.921	6.664	-29.097	-29.097	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.965	-0.970	5.772	-33.686	-33.686	0.000	0.000	0.000	0.000
59	A	62	ILE	0	-0.094	-0.062	2.191	-14.900	-14.343	2.725	-1.084	-2.199	-0.007
60	A	63	GLY	0	0.019	0.019	2.248	-17.885	-17.066	4.202	-1.909	-3.111	-0.037
61	A	64	VAL	0	-0.014	-0.013	3.371	7.762	8.164	0.011	-0.076	-0.337	0.000
62	A	65	GLY	0	0.027	0.012	5.805	-2.538	-2.538	0.000	0.000	0.000	0.000
63	A	66	TYR	0	-0.021	-0.002	8.492	2.136	2.136	0.000	0.000	0.000	0.000
64	A	67	VAL	0	0.010	0.002	11.873	-0.370	-0.370	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.816	0.888	14.311	17.333	17.333	0.000	0.000	0.000	0.000
66	A	69	ASP	-1	-0.906	-0.942	17.488	-13.276	-13.276	0.000	0.000	0.000	0.000
67	A	70	ARG	1	0.840	0.898	19.545	15.140	15.140	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.086	0.059	23.116	0.323	0.323	0.000	0.000	0.000	0.000
69	A	72	SER	0	-0.036	-0.020	24.782	-0.389	-0.389	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.057	-0.029	20.448	-0.160	-0.160	0.000	0.000	0.000	0.000
71	A	74	SER	0	0.035	0.021	18.201	0.188	0.188	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.775	-0.885	15.685	-17.267	-17.267	0.000	0.000	0.000	0.000
73	A	76	TYR	0	-0.016	0.006	5.828	-0.123	-0.123	0.000	0.000	0.000	0.000
74	A	77	ILE	0	0.017	-0.006	11.820	0.044	0.044	0.000	0.000	0.000	0.000
75	A	78	LEU	0	-0.039	-0.005	5.843	0.257	0.257	0.000	0.000	0.000	0.000
76	A	79	SER	0	-0.018	-0.032	9.001	1.834	1.834	0.000	0.000	0.000	0.000
77	A	80	GLU	-1	-0.824	-0.934	11.177	-20.653	-20.653	0.000	0.000	0.000	0.000
78	A	81	ILE	0	0.099	0.038	10.880	-2.050	-2.050	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.938	0.997	9.874	19.252	19.252	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.020	0.011	5.450	-1.333	-1.333	0.000	0.000	0.000	0.000
81	A	84	LEU	0	-0.006	-0.008	5.487	-7.179	-7.179	0.000	0.000	0.000	0.000
82	A	85	HIS	0	0.045	0.023	7.528	-1.330	-1.330	0.000	0.000	0.000	0.000
83	A	86	ASN	0	0.000	0.014	2.625	-16.059	-13.717	0.866	-1.243	-1.965	-0.016
84	A	87	PHE	0	0.027	0.012	2.454	-6.868	-5.978	0.420	-0.265	-1.045	-0.002
85	A	88	LEU	0	0.043	0.025	3.961	2.647	2.753	-0.001	-0.020	-0.086	0.000
86	A	89	THR	0	-0.005	-0.019	7.516	2.985	2.985	0.000	0.000	0.000	0.000
87	A	90	GLN	0	-0.030	-0.022	3.016	4.006	5.163	0.043	-0.539	-0.661	0.000
88	A	91	LEU	0	-0.022	0.010	5.820	2.027	2.027	0.000	0.000	0.000	0.000
89	A	92	GLN	0	0.024	-0.002	7.607	3.916	3.916	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.037	0.027	9.942	2.160	2.160	0.000	0.000	0.000	0.000
91	A	94	PHE	0	-0.067	-0.039	8.577	1.754	1.754	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.009	-0.057	12.626	0.593	0.593	0.000	0.000	0.000	0.000
93	A	96	LYS	1	0.970	0.992	14.537	16.900	16.900	0.000	0.000	0.000	0.000
94	A	97	LEU	0	-0.024	-0.005	17.225	0.916	0.916	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.767	0.874	15.001	18.886	18.886	0.000	0.000	0.000	0.000
96	A	99	GLN	0	-0.073	-0.010	11.736	-1.843	-1.843	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.947	0.998	14.988	14.682	14.682	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.081	0.007	16.193	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	102	ALA	0	0.023	0.038	11.868	-0.615	-0.615	0.000	0.000	0.000	0.000
100	A	103	ASN	0	0.018	-0.003	13.463	-0.817	-0.817	0.000	0.000	0.000	0.000
101	A	104	LEU	0	0.006	0.014	15.367	0.094	0.094	0.000	0.000	0.000	0.000
102	A	105	VAL	0	0.004	0.001	13.076	0.542	0.542	0.000	0.000	0.000	0.000
103	A	106	LEU	0	-0.028	-0.027	9.903	-0.142	-0.142	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.852	0.959	13.808	14.823	14.823	0.000	0.000	0.000	0.000
105	A	108	ILE	0	0.030	0.012	17.549	0.531	0.531	0.000	0.000	0.000	0.000
106	A	109	ILE	0	-0.154	-0.060	11.675	0.062	0.062	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.897	-0.958	15.365	-18.720	-18.720	0.000	0.000	0.000	0.000
108	A	111	GLN	0	-0.088	-0.048	17.783	1.379	1.379	0.000	0.000	0.000	0.000
109	A	112	LEU	0	0.020	0.012	18.319	0.454	0.454	0.000	0.000	0.000	0.000
110	A	113	PRO	0	-0.031	0.003	22.383	0.256	0.256	0.000	0.000	0.000	0.000
111	A	123	LEU	0	0.012	-0.023	29.667	0.081	0.081	0.000	0.000	0.000	0.000
112	A	124	GLU	-1	-0.885	-0.913	26.347	-11.646	-11.646	0.000	0.000	0.000	0.000
113	A	125	VAL	0	0.013	0.011	24.796	-0.531	-0.531	0.000	0.000	0.000	0.000
114	A	126	CYS	0	-0.087	-0.065	23.948	0.374	0.374	0.000	0.000	0.000	0.000
115	A	127	THR	0	0.021	0.011	24.830	0.200	0.200	0.000	0.000	0.000	0.000
116	A	128	TRP	0	0.069	0.013	21.495	-0.083	-0.083	0.000	0.000	0.000	0.000
117	A	129	VAL	0	0.018	-0.005	21.157	-0.249	-0.249	0.000	0.000	0.000	0.000
118	A	130	ASP	-1	-0.884	-0.918	22.827	-11.707	-11.707	0.000	0.000	0.000	0.000
119	A	131	GLN	0	0.002	-0.006	23.993	-0.363	-0.363	0.000	0.000	0.000	0.000
120	A	132	ILE	0	-0.111	-0.043	18.534	-0.338	-0.338	0.000	0.000	0.000	0.000
121	A	133	ALA	0	0.062	0.027	22.352	-0.287	-0.287	0.000	0.000	0.000	0.000
122	A	134	ALA	0	-0.118	-0.055	21.302	0.108	0.108	0.000	0.000	0.000	0.000
123	A	135	LEU	0	-0.025	-0.035	23.328	-0.168	-0.168	0.000	0.000	0.000	0.000
124	A	136	ASN	0	-0.049	0.000	22.158	0.153	0.153	0.000	0.000	0.000	0.000
125	A	137	ASP	-1	-0.881	-0.947	26.562	-10.063	-10.063	0.000	0.000	0.000	0.000
126	A	138	SER	0	-0.060	-0.020	28.611	0.167	0.167	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)