FMO DATABASE

FMODB ID: G6GR1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1174546.009513
FMO2-HF: Nuclear repulsion	1117752.371105
FMO2-HF: Total energy	-56793.638408
FMO2-MP2: Total energy	-56960.942271

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.
-94.241	-112.283	65.116	-28.574	-18.5	0.106

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 : -0.752 / q_NPA : -0.830

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	-0.019	-0.013	3.314	-9.315	-6.361	-0.016	-1.521	-1.417	0.002
4	A	4	LEU	0	0.067	0.041	2.909	-4.845	-3.868	0.032	-0.389	-0.620	0.001
5	A	5	ILE	0	-0.032	-0.002	1.813	4.121	0.805	14.074	-5.985	-4.773	-0.035
6	A	6	VAL	0	-0.013	-0.001	4.029	-8.042	-7.825	0.000	-0.078	-0.139	0.000
7	A	7	PHE	0	-0.020	-0.023	5.373	-4.787	-4.787	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.795	-0.906	7.250	22.942	22.942	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.039	-0.025	10.357	0.795	0.795	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.792	-0.859	12.481	22.010	22.010	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.004	-0.012	11.785	1.913	1.913	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.902	0.941	12.073	-21.553	-21.553	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.013	0.010	7.617	2.064	2.064	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.002	-0.005	7.595	6.311	6.311	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.928	-0.968	7.219	31.050	31.050	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.029	0.027	8.201	-0.139	-0.139	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.120	-0.070	3.093	-2.619	-1.446	0.104	-0.549	-0.727	0.006
18	A	18	TYR	0	-0.024	-0.059	1.606	-23.617	-31.503	22.667	-8.766	-6.016	0.074
19	A	19	HIS	1	0.842	0.933	5.016	-41.739	-41.735	-0.001	-0.003	0.000	0.000
20	A	20	ASN	0	-0.054	-0.039	5.844	-7.339	-7.339	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.028	-0.025	1.514	-21.525	-35.468	28.086	-10.717	-3.425	0.061
22	A	22	SER	0	0.004	-0.012	4.302	-8.511	-8.324	-0.001	-0.051	-0.135	0.000
23	A	23	TRP	0	0.103	0.058	4.693	1.753	2.008	-0.001	-0.012	-0.243	0.000
24	A	24	ARG	1	0.956	0.992	5.518	-28.121	-28.097	-0.001	0.000	-0.023	0.000
25	A	25	ASN	0	-0.005	-0.021	8.996	-2.211	-2.211	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.084	0.054	5.293	-2.130	-2.130	0.000	0.000	0.000	0.000
27	A	27	TYR	0	0.022	-0.010	6.220	-2.524	-2.524	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.025	-0.018	8.676	-3.006	-3.006	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.822	-0.916	7.890	24.194	24.194	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.015	0.009	6.897	-1.186	-1.186	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.001	0.010	9.729	-1.368	-1.368	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.854	0.911	11.474	-24.282	-24.282	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.049	-0.004	10.719	-1.242	-1.242	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.002	0.008	12.850	-1.252	-1.252	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.005	-0.014	15.201	-0.674	-0.674	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.905	0.948	13.051	-19.309	-19.309	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.016	0.000	14.001	-1.367	-1.367	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.795	0.857	18.666	-12.057	-12.057	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.004	0.015	16.620	-0.516	-0.516	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.005	-0.003	19.656	0.031	0.031	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.063	-0.054	18.884	0.238	0.238	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.010	0.021	19.955	0.049	0.049	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.020	-0.006	17.724	-0.329	-0.329	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.012	0.011	14.561	0.386	0.386	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.010	-0.008	10.424	-0.290	-0.290	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.045	0.017	10.631	0.097	0.097	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.028	-0.016	2.978	0.253	1.565	0.173	-0.503	-0.982	-0.003
48	A	48	LEU	0	-0.022	-0.005	7.845	-1.698	-1.698	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.002	-0.008	6.819	2.476	2.476	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.801	-0.890	6.346	31.241	31.241	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.840	0.903	9.350	-24.531	-24.531	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.071	0.059	11.343	-1.504	-1.504	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.062	0.029	11.070	2.078	2.078	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.896	0.949	10.670	-23.305	-23.305	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.037	0.010	13.158	0.643	0.643	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.037	0.026	13.552	-0.106	-0.106	0.000	0.000	0.000	0.000
57	A	57	HIS	0	0.032	0.013	7.528	-0.610	-0.610	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.040	0.034	11.955	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.029	-0.006	14.841	-0.234	-0.234	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.035	-0.015	11.899	-0.328	-0.328	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.043	0.022	12.743	-0.383	-0.383	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.013	-0.009	14.366	-0.738	-0.738	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.025	0.010	16.973	-0.091	-0.091	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.931	-0.958	11.996	20.112	20.112	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.083	-0.046	16.731	-0.614	-0.614	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.012	0.005	19.337	-0.613	-0.613	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.036	-0.014	17.577	-0.486	-0.486	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.893	0.955	18.486	-14.441	-14.441	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.042	-0.016	21.976	-0.485	-0.485	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.072	0.028	24.960	-0.260	-0.260	0.000	0.000	0.000	0.000
71	A	71	TRP	0	0.025	0.006	27.050	-0.050	-0.050	0.000	0.000	0.000	0.000
72	A	72	PHE	0	-0.017	-0.009	20.996	-0.175	-0.175	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.854	-0.910	24.835	11.347	11.347	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.866	0.924	25.841	-8.942	-8.942	0.000	0.000	0.000	0.000
75	A	75	CYS	0	-0.034	-0.014	25.836	-0.306	-0.306	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.057	0.034	21.427	0.059	0.059	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.010	-0.014	24.168	0.126	0.126	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.085	-0.036	26.980	-0.632	-0.632	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.044	-0.009	23.776	-0.217	-0.217	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.011	0.005	22.980	0.608	0.608	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.018	-0.009	18.959	0.741	0.741	0.000	0.000	0.000	0.000
82	A	82	TYR	0	0.001	-0.007	20.982	-0.622	-0.622	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.900	-0.941	20.250	14.421	14.421	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.039	-0.013	15.963	-0.184	-0.184	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.037	-0.032	19.726	-0.626	-0.626	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.893	-0.956	16.956	16.669	16.669	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.828	-0.871	19.212	11.569	11.569	0.000	0.000	0.000	0.000
88	A	88	PHE	0	-0.014	0.005	20.291	-0.663	-0.663	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.006	-0.013	19.564	1.054	1.054	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.032	-0.006	17.310	-0.316	-0.316	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.014	-0.003	19.321	0.051	0.051	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.095	0.049	23.066	-0.176	-0.176	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.004	0.012	18.689	-0.181	-0.181	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.018	-0.004	21.656	-0.103	-0.103	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.863	-0.921	23.757	10.230	10.230	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.008	0.006	25.036	-0.345	-0.345	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.011	-0.012	22.147	-0.281	-0.281	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.017	-0.024	25.333	-0.342	-0.342	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.021	-0.004	28.492	-0.448	-0.448	0.000	0.000	0.000	0.000
100	A	100	ALA	0	0.001	-0.008	26.858	-0.283	-0.283	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.813	0.884	28.808	-9.342	-9.342	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.828	-0.896	30.217	8.500	8.500	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.070	-0.020	31.470	-0.321	-0.321	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.016	-0.001	30.712	-0.214	-0.214	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.786	-0.893	32.829	8.494	8.494	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.901	0.945	34.810	-8.553	-8.553	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.902	0.955	30.083	-9.618	-9.618	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.020	0.008	34.424	-0.163	-0.163	0.000	0.000	0.000	0.000
109	A	109	GLY	0	-0.006	-0.002	37.985	-0.194	-0.194	0.000	0.000	0.000	0.000
110	A	110	MET	0	-0.026	-0.011	39.621	-0.116	-0.116	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.014	0.002	37.614	-0.148	-0.148	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.800	0.886	40.792	-7.394	-7.394	0.000	0.000	0.000	0.000
113	A	113	HIS	0	0.031	0.011	43.820	-0.191	-0.191	0.000	0.000	0.000	0.000
114	A	114	GLN	0	0.037	0.014	42.295	-0.023	-0.023	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.035	-0.010	43.294	-0.063	-0.063	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.041	-0.014	47.154	-0.117	-0.117	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.929	-0.962	49.113	6.112	6.112	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.077	-0.033	48.964	-0.092	-0.092	0.000	0.000	0.000	0.000
119	A	119	GLY	0	-0.009	0.003	50.962	-0.077	-0.077	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.081	-0.039	47.266	-0.063	-0.063	0.000	0.000	0.000	0.000
121	A	121	THR	0	-0.020	-0.048	51.087	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	SER	0	0.029	-0.014	49.726	0.090	0.090	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.773	-0.855	48.065	6.077	6.077	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.838	0.927	46.729	-5.904	-5.904	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.016	0.010	44.965	0.169	0.169	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.874	-0.912	42.754	7.223	7.223	0.000	0.000	0.000	0.000
127	A	127	GLU	-1	-0.885	-0.944	42.045	6.577	6.577	0.000	0.000	0.000	0.000
128	A	128	ILE	0	0.014	0.004	41.655	0.189	0.189	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.008	0.002	37.421	0.196	0.196	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.023	0.017	37.632	0.251	0.251	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.020	-0.008	38.155	0.276	0.276	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.025	-0.012	35.854	0.281	0.281	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.812	0.898	32.853	-8.135	-8.135	0.000	0.000	0.000	0.000
134	A	134	PHE	0	0.021	0.021	31.702	0.299	0.299	0.000	0.000	0.000	0.000
135	A	135	SER	0	0.006	-0.024	28.616	-0.243	-0.243	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.023	-0.002	29.403	0.139	0.139	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.863	-0.936	25.311	11.348	11.348	0.000	0.000	0.000	0.000
138	A	138	ASN	0	-0.096	-0.057	23.020	0.498	0.498	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.021	0.011	25.885	-0.399	-0.399	0.000	0.000	0.000	0.000

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