FMO DATABASE

FMODB ID: V5LN1

Calculation Name: 5DYR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DYR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PHF6

Base Structure: X-ray

Registration Date: 2023-09-19

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1174186.24515
FMO2-HF: Nuclear repulsion	1117395.27453
FMO2-HF: Total energy	-56790.97062
FMO2-MP2: Total energy	-56958.540476

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:ASP)

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

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.
-53.368	-51.76	29.032	-15.78	-14.86	0.04

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.824 / q_NPA : -0.910

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	CYS	0	-0.004	-0.008	3.853	-7.373	-5.324	-0.013	-0.961	-1.075	0.003
4	A	4	LEU	0	0.086	0.045	2.858	-4.846	-3.909	0.035	-0.389	-0.582	0.001
5	A	5	ILE	0	-0.042	0.002	1.887	2.257	-0.320	12.811	-5.058	-5.176	-0.021
6	A	6	VAL	0	-0.017	-0.001	3.924	-5.493	-5.376	0.000	-0.043	-0.075	0.000
7	A	7	PHE	0	-0.035	-0.030	6.298	-3.246	-3.246	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.860	-0.936	7.906	22.323	22.323	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.033	-0.022	10.809	1.163	1.163	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.858	-0.922	12.495	21.844	21.844	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.036	-0.001	11.832	1.782	1.782	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.958	0.981	12.080	-20.416	-20.416	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.001	0.017	8.176	2.144	2.144	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.013	0.018	7.491	7.001	7.001	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.958	-0.969	7.236	29.160	29.160	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.019	0.021	7.618	-1.499	-1.499	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.081	-0.054	3.164	-1.863	-0.699	0.072	-0.547	-0.690	0.005
18	A	18	TYR	0	0.038	0.003	3.296	12.294	14.087	0.285	-0.594	-1.484	0.001
19	A	19	HIS	1	0.871	0.944	5.160	-50.097	-50.120	-0.001	-0.003	0.027	0.000
20	A	20	ASN	0	-0.071	-0.048	5.640	-0.990	-0.990	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.027	-0.027	1.700	-22.546	-26.484	15.657	-7.428	-4.291	0.053
22	A	22	SER	0	0.013	-0.010	3.929	-11.893	-11.647	0.000	-0.124	-0.122	0.001
23	A	23	TRP	0	0.105	0.065	4.209	6.609	7.006	0.000	-0.034	-0.364	0.000
24	A	24	ARG	1	0.971	0.991	5.755	-27.277	-27.256	-0.001	0.000	-0.019	0.000
25	A	25	ASN	0	0.016	-0.007	8.506	-2.898	-2.898	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.087	0.052	5.212	-1.799	-1.799	0.000	0.000	0.000	0.000
27	A	27	TYR	0	0.041	0.009	5.924	-2.264	-2.264	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.056	-0.035	8.751	-3.083	-3.083	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.937	-0.999	7.210	27.217	27.217	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.006	0.027	6.904	-0.570	-0.570	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.021	0.009	9.652	-0.994	-0.994	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.905	0.951	11.951	-22.492	-22.492	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.030	-0.005	10.714	-1.370	-1.370	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.012	0.028	12.836	-1.126	-1.126	0.000	0.000	0.000	0.000
35	A	35	TYR	0	0.001	-0.004	15.322	-0.736	-0.736	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.925	0.958	13.343	-18.576	-18.576	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.000	-0.009	14.602	-1.137	-1.137	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.872	0.942	18.647	-12.056	-12.056	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.047	-0.015	16.341	-0.400	-0.400	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.031	0.013	19.541	-0.076	-0.076	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.048	-0.040	18.791	0.076	0.076	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.009	0.024	19.846	-0.051	-0.051	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.017	-0.017	18.339	-0.601	-0.601	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.028	0.007	14.328	0.274	0.274	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.001	-0.001	9.630	-0.438	-0.438	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.063	0.018	10.875	0.275	0.275	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.051	-0.029	3.042	-0.168	1.254	0.187	-0.599	-1.009	-0.003
48	A	48	LEU	0	-0.035	-0.004	8.045	-0.630	-0.630	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.013	-0.010	6.360	2.485	2.485	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.926	-0.974	6.565	31.628	31.628	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.863	0.920	8.960	-25.043	-25.043	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.077	0.060	10.744	-1.572	-1.572	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.091	0.037	10.689	2.108	2.108	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.885	0.954	10.208	-23.985	-23.985	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.073	0.025	13.179	-0.160	-0.160	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.016	0.010	13.009	-0.089	-0.089	0.000	0.000	0.000	0.000
57	A	57	HIS	0	0.069	0.011	7.523	-0.463	-0.463	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.035	0.041	12.206	-0.447	-0.447	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.058	0.009	14.672	-0.791	-0.791	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.045	-0.030	11.587	-0.301	-0.301	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.021	-0.001	13.205	-0.173	-0.173	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.002	-0.006	14.540	-0.689	-0.689	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.014	0.005	17.248	0.242	0.242	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.924	-0.954	12.448	19.397	19.397	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.112	-0.058	17.207	-0.659	-0.659	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.027	0.004	19.668	-0.669	-0.669	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.009	0.004	18.055	-0.461	-0.461	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.879	0.955	19.388	-14.063	-14.063	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.057	-0.028	22.025	-0.495	-0.495	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.092	0.041	25.104	-0.122	-0.122	0.000	0.000	0.000	0.000
71	A	71	TRP	0	0.036	0.009	26.923	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.004	0.002	22.186	-0.166	-0.166	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.869	-0.932	25.371	11.383	11.383	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.963	0.995	26.430	-8.738	-8.738	0.000	0.000	0.000	0.000
75	A	75	CYS	0	-0.011	-0.007	26.053	-0.236	-0.236	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.053	0.045	22.046	0.180	0.180	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.029	-0.019	24.557	0.036	0.036	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.145	-0.095	27.458	-0.358	-0.358	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.036	-0.007	23.833	-0.212	-0.212	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.023	0.014	23.212	0.617	0.617	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.037	-0.024	19.115	0.679	0.679	0.000	0.000	0.000	0.000
82	A	82	TYR	0	0.023	-0.004	20.875	-0.510	-0.510	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.972	-0.960	20.106	14.227	14.227	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.023	-0.018	15.959	-0.245	-0.245	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.006	-0.007	19.944	-0.498	-0.498	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.929	-0.967	17.895	15.701	15.701	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.887	-0.949	19.159	11.779	11.779	0.000	0.000	0.000	0.000
88	A	88	PHE	0	-0.029	-0.003	20.057	-0.750	-0.750	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.023	-0.009	19.590	0.904	0.904	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.068	0.018	17.621	-0.163	-0.163	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.042	-0.022	19.457	-0.056	-0.056	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.097	0.043	23.117	-0.179	-0.179	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.014	0.004	18.587	-0.197	-0.197	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.056	-0.029	21.831	-0.052	-0.052	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.873	-0.933	23.810	10.044	10.044	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.008	0.012	25.333	-0.373	-0.373	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.060	0.016	22.689	-0.292	-0.292	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.013	0.011	25.835	-0.299	-0.299	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.037	-0.014	28.960	-0.400	-0.400	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.038	0.003	27.127	-0.274	-0.274	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.882	0.914	29.055	-9.285	-9.285	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.919	-0.946	30.575	8.194	8.194	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.051	-0.031	31.862	-0.297	-0.297	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.012	-0.011	30.984	-0.204	-0.204	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.850	-0.936	33.111	8.410	8.410	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.939	0.958	35.322	-8.457	-8.457	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.905	0.961	30.973	-9.445	-9.445	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.019	0.009	34.976	-0.153	-0.153	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.000	-0.008	38.295	-0.177	-0.177	0.000	0.000	0.000	0.000
110	A	110	MET	0	0.000	0.004	39.919	-0.090	-0.090	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.025	-0.002	38.393	-0.154	-0.154	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.914	0.962	40.253	-7.530	-7.530	0.000	0.000	0.000	0.000
113	A	113	HIS	0	0.035	0.012	44.132	-0.214	-0.214	0.000	0.000	0.000	0.000
114	A	114	GLN	0	0.049	0.043	42.315	-0.065	-0.065	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.043	-0.020	43.829	-0.062	-0.062	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.022	-0.012	47.555	-0.102	-0.102	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.940	-0.966	49.585	6.113	6.113	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.108	-0.032	49.056	-0.062	-0.062	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.018	-0.009	51.126	-0.120	-0.120	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.089	-0.049	47.182	-0.078	-0.078	0.000	0.000	0.000	0.000
121	A	121	THR	0	0.055	0.030	51.329	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	122	SER	0	0.054	0.013	49.876	0.086	0.086	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.865	-0.916	48.383	6.064	6.064	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.971	0.975	47.311	-5.810	-5.810	0.000	0.000	0.000	0.000
125	A	125	ILE	0	-0.087	-0.029	45.088	0.168	0.168	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.965	-1.002	43.399	6.848	6.848	0.000	0.000	0.000	0.000
127	A	127	GLU	-1	-0.943	-0.957	42.755	6.646	6.646	0.000	0.000	0.000	0.000
128	A	128	ILE	0	-0.022	-0.019	41.967	0.193	0.193	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.037	-0.015	37.774	0.208	0.208	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.009	-0.011	37.851	0.251	0.251	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.050	-0.007	38.418	0.112	0.112	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.027	-0.015	35.670	0.329	0.329	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.929	0.972	33.041	-8.560	-8.560	0.000	0.000	0.000	0.000
134	A	134	PHE	0	0.008	0.011	31.513	0.196	0.196	0.000	0.000	0.000	0.000
135	A	135	SER	0	-0.021	-0.023	29.073	-0.293	-0.293	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.045	-0.014	29.645	0.094	0.094	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.860	-0.930	25.505	11.501	11.501	0.000	0.000	0.000	0.000
138	A	138	ASN	0	-0.047	-0.042	22.962	0.156	0.156	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.042	-0.009	25.820	-0.397	-0.397	0.000	0.000	0.000	0.000

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