FMO DATABASE

FMODB ID: 17KYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1174637.898474
FMO2-HF: Nuclear repulsion	1117845.585912
FMO2-HF: Total energy	-56792.312562
FMO2-MP2: Total energy	-56959.768673

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.
-79.956	-86.49	51.094	-24.648	-19.912	0.087

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 : -0.776 / q_NPA : -0.868

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	-0.018	-0.012	3.766	-7.790	-5.698	-0.014	-0.980	-1.098	0.003
4	A	4	LEU	0	0.082	0.038	2.804	-4.875	-3.926	0.043	-0.387	-0.605	0.001
5	A	5	ILE	0	-0.056	-0.005	1.889	4.028	1.944	13.506	-5.864	-5.558	-0.026
6	A	6	VAL	0	0.000	0.018	3.968	-6.736	-6.608	0.000	-0.047	-0.082	0.000
7	A	7	PHE	0	-0.049	-0.048	5.945	-3.811	-3.811	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.803	-0.917	7.670	22.473	22.473	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.044	-0.019	10.626	1.151	1.151	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.823	-0.878	12.517	22.039	22.039	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.038	-0.006	11.836	1.740	1.740	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.900	0.931	12.071	-20.958	-20.958	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.013	0.016	7.916	1.930	1.930	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.027	0.020	7.449	6.669	6.669	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.957	-0.970	7.196	29.876	29.876	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.042	0.033	8.053	-0.978	-0.978	0.000	0.000	0.000	0.000
17	A	17	HIS	0	-0.107	-0.079	3.423	-1.367	-0.616	0.026	-0.326	-0.450	0.002
18	A	18	TYR	0	-0.023	-0.033	1.865	-10.305	-9.370	9.441	-4.654	-5.722	0.050
19	A	19	HIS	1	0.862	0.958	4.967	-44.558	-44.561	-0.001	-0.004	0.008	0.000
20	A	20	ASN	0	-0.078	-0.058	5.481	-7.134	-7.134	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.030	-0.038	1.539	-25.026	-36.640	27.616	-11.435	-4.567	0.063
22	A	22	SER	0	-0.008	-0.008	4.197	-11.872	-11.624	0.000	-0.095	-0.153	0.000
23	A	23	TRP	0	0.125	0.061	4.280	6.306	6.684	0.000	-0.032	-0.346	0.000
24	A	24	ARG	1	0.978	1.001	5.707	-27.532	-27.510	-0.001	0.000	-0.021	0.000
25	A	25	ASN	0	0.006	-0.012	8.740	-2.320	-2.320	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.082	0.054	5.215	-1.976	-1.976	0.000	0.000	0.000	0.000
27	A	27	TYR	0	0.037	-0.003	5.934	-2.300	-2.300	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.040	-0.028	8.746	-3.028	-3.028	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.865	-0.941	7.423	24.827	24.827	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.002	0.025	7.083	-0.677	-0.677	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.025	0.017	9.639	-1.258	-1.258	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.841	0.898	11.496	-24.035	-24.035	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.024	0.000	10.795	-1.367	-1.367	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.004	0.022	12.873	-1.139	-1.139	0.000	0.000	0.000	0.000
35	A	35	TYR	0	0.005	-0.002	15.305	-0.701	-0.701	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.926	0.960	13.124	-19.080	-19.080	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.013	-0.011	14.202	-1.276	-1.276	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.798	0.866	18.631	-12.103	-12.103	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.042	-0.010	16.654	-0.424	-0.424	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.013	0.001	19.519	-0.210	-0.210	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.051	-0.044	18.791	0.191	0.191	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.001	0.033	19.856	-0.070	-0.070	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.014	-0.016	17.801	-0.450	-0.450	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.026	0.006	14.328	0.264	0.264	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.003	-0.001	10.105	-0.393	-0.393	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.051	0.014	10.829	0.304	0.304	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.051	-0.030	2.732	0.227	1.891	0.478	-0.824	-1.318	-0.006
48	A	48	LEU	0	-0.025	0.007	8.020	-0.628	-0.628	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.031	-0.032	6.363	2.436	2.436	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.804	-0.893	6.245	32.494	32.494	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.836	0.898	9.014	-24.973	-24.973	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.095	0.072	10.763	-1.540	-1.540	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.084	0.041	10.681	2.206	2.206	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.848	0.924	10.345	-23.744	-23.744	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.081	0.029	13.179	0.017	0.017	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.026	0.016	13.068	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	57	HIS	0	0.101	0.044	7.518	-0.647	-0.647	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.026	0.040	12.142	-0.406	-0.406	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.052	0.002	14.614	-0.330	-0.330	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.031	-0.024	11.795	-0.262	-0.262	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.023	-0.008	13.003	-0.194	-0.194	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.006	-0.008	14.484	-0.674	-0.674	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.014	0.005	17.382	0.051	0.051	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.913	-0.951	12.327	19.621	19.621	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.128	-0.062	17.156	-0.660	-0.660	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.029	0.007	19.620	-0.655	-0.655	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.021	-0.001	17.877	-0.451	-0.451	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.889	0.953	18.936	-14.337	-14.337	0.000	0.000	0.000	0.000
69	A	69	PHE	0	-0.044	-0.017	22.403	-0.513	-0.513	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.086	0.038	25.054	-0.134	-0.134	0.000	0.000	0.000	0.000
71	A	71	TRP	0	0.029	0.008	27.224	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	72	PHE	0	-0.020	-0.007	21.305	-0.178	-0.178	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.876	-0.935	25.316	11.267	11.267	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.909	0.953	26.373	-8.678	-8.678	0.000	0.000	0.000	0.000
75	A	75	CYS	0	-0.002	0.001	26.190	-0.238	-0.238	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.044	0.041	21.844	0.184	0.184	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.011	-0.005	24.496	0.067	0.067	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.118	-0.075	27.396	-0.275	-0.275	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.047	-0.015	23.708	-0.190	-0.190	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.002	0.031	23.163	0.691	0.691	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.050	-0.033	19.189	0.675	0.675	0.000	0.000	0.000	0.000
82	A	82	TYR	0	0.010	-0.009	21.029	-0.541	-0.541	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.946	-0.948	20.052	14.245	14.245	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.019	-0.014	15.988	-0.257	-0.257	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.019	-0.016	19.925	-0.510	-0.510	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.911	-0.963	17.137	16.298	16.298	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.842	-0.889	19.145	11.551	11.551	0.000	0.000	0.000	0.000
88	A	88	PHE	0	0.002	0.010	20.043	-0.707	-0.707	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.039	-0.019	19.559	0.959	0.959	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.071	0.022	17.580	-0.163	-0.163	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.019	-0.009	19.424	-0.078	-0.078	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.094	0.044	23.110	-0.160	-0.160	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.009	-0.001	18.537	-0.212	-0.212	0.000	0.000	0.000	0.000
94	A	94	ILE	0	-0.058	-0.035	21.789	-0.065	-0.065	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.849	-0.928	23.766	10.173	10.173	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.017	0.015	25.283	-0.382	-0.382	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.044	0.014	22.506	-0.293	-0.293	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.006	0.013	25.783	-0.307	-0.307	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.024	-0.005	28.909	-0.420	-0.420	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.026	-0.009	27.061	-0.276	-0.276	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.843	0.895	29.000	-9.290	-9.290	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.855	-0.908	30.518	8.372	8.372	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.056	-0.037	31.823	-0.295	-0.295	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.006	-0.010	30.935	-0.208	-0.208	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.830	-0.915	33.052	8.442	8.442	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.928	0.952	35.023	-8.496	-8.496	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.903	0.963	30.731	-9.491	-9.491	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.025	0.012	34.705	-0.148	-0.148	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.011	-0.001	38.233	-0.175	-0.175	0.000	0.000	0.000	0.000
110	A	110	MET	0	-0.012	0.001	39.758	-0.095	-0.095	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.033	0.008	38.140	-0.149	-0.149	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.805	0.891	41.337	-7.373	-7.373	0.000	0.000	0.000	0.000
113	A	113	HIS	0	0.038	0.013	44.069	-0.194	-0.194	0.000	0.000	0.000	0.000
114	A	114	GLN	0	0.043	0.032	42.712	-0.025	-0.025	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.042	-0.017	43.774	-0.066	-0.066	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.031	-0.016	47.491	-0.105	-0.105	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.943	-0.962	49.606	6.091	6.091	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.113	-0.038	48.980	-0.063	-0.063	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.014	-0.010	51.061	-0.121	-0.121	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.098	-0.046	47.404	-0.070	-0.070	0.000	0.000	0.000	0.000
121	A	121	THR	0	0.078	0.038	51.264	-0.028	-0.028	0.000	0.000	0.000	0.000
122	A	122	SER	0	0.030	-0.016	49.812	0.100	0.100	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.854	-0.902	48.321	6.039	6.039	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.979	0.982	47.247	-5.791	-5.791	0.000	0.000	0.000	0.000
125	A	125	ILE	0	-0.067	-0.023	45.343	0.169	0.169	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.888	-0.939	43.335	7.163	7.163	0.000	0.000	0.000	0.000
127	A	127	GLU	-1	-0.940	-0.961	42.692	6.615	6.615	0.000	0.000	0.000	0.000
128	A	128	ILE	0	-0.020	-0.021	41.931	0.188	0.188	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.008	-0.001	37.830	0.197	0.197	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.001	-0.004	37.788	0.246	0.246	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.030	-0.002	38.354	0.194	0.194	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.031	-0.027	35.902	0.291	0.291	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.891	0.964	32.965	-8.263	-8.263	0.000	0.000	0.000	0.000
134	A	134	PHE	0	0.011	0.014	31.840	0.210	0.210	0.000	0.000	0.000	0.000
135	A	135	SER	0	-0.013	-0.032	28.874	-0.293	-0.293	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.058	-0.020	29.696	0.097	0.097	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.860	-0.931	25.482	11.368	11.368	0.000	0.000	0.000	0.000
138	A	138	ASN	0	-0.061	-0.049	22.638	0.310	0.310	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.026	0.002	25.820	-0.390	-0.390	0.000	0.000	0.000	0.000

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