FMO DATABASE

FMODB ID: 7227K

Calculation Name: 5DPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DPR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H492

Base Structure: X-ray

Registration Date: 2023-06-21

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1105056.451943
FMO2-HF: Nuclear repulsion	1054132.261697
FMO2-HF: Total energy	-50924.190246
FMO2-MP2: Total energy	-51073.198249

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:6:GLU)

Summations of interaction energy for fragment #1(A:6:GLU)

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.
-38.639	-36.995	-0.015	-0.786	-0.843	0.005

Interaction energy analysis for fragmet #1(A:6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.947 / q_NPA : -0.983

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	8	VAL	0	0.005	-0.001	3.804	-3.626	-1.982	-0.015	-0.786	-0.843	0.005
4	A	9	ASN	0	-0.033	-0.020	6.492	-2.610	-2.610	0.000	0.000	0.000	0.000
5	A	10	VAL	0	0.003	0.002	9.371	-1.399	-1.399	0.000	0.000	0.000	0.000
6	A	11	GLY	0	-0.017	0.015	12.511	-0.583	-0.583	0.000	0.000	0.000	0.000
7	A	12	SER	0	0.087	0.021	15.599	0.506	0.506	0.000	0.000	0.000	0.000
8	A	13	PRO	0	-0.053	-0.040	18.803	-0.319	-0.319	0.000	0.000	0.000	0.000
9	A	14	SER	0	0.021	0.015	22.049	-0.373	-0.373	0.000	0.000	0.000	0.000
10	A	15	ASP	-1	-0.891	-0.948	19.496	13.549	13.549	0.000	0.000	0.000	0.000
11	A	16	ARG	1	0.925	0.972	19.528	-13.273	-13.273	0.000	0.000	0.000	0.000
12	A	17	PRO	0	0.037	0.021	22.865	-0.336	-0.336	0.000	0.000	0.000	0.000
13	A	18	PHE	0	0.050	0.003	26.326	0.108	0.108	0.000	0.000	0.000	0.000
14	A	19	LYS	1	0.792	0.878	29.323	-8.621	-8.621	0.000	0.000	0.000	0.000
15	A	20	GLN	0	-0.015	-0.011	23.655	0.236	0.236	0.000	0.000	0.000	0.000
16	A	21	ARG	1	0.763	0.885	25.667	-10.630	-10.630	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.869	0.939	27.577	-8.798	-8.798	0.000	0.000	0.000	0.000
18	A	23	SER	0	0.037	0.001	31.197	-0.072	-0.072	0.000	0.000	0.000	0.000
19	A	24	PHE	0	0.092	0.027	32.896	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.071	0.039	35.721	-0.182	-0.182	0.000	0.000	0.000	0.000
21	A	26	ASP	-1	-0.856	-0.910	34.687	8.270	8.270	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.768	0.876	32.535	-8.842	-8.842	0.000	0.000	0.000	0.000
23	A	28	CYS	0	0.013	0.028	37.146	-0.136	-0.136	0.000	0.000	0.000	0.000
24	A	29	LYS	1	0.859	0.931	38.371	-7.892	-7.892	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.826	-0.901	36.272	8.285	8.285	0.000	0.000	0.000	0.000
26	A	31	VAL	0	-0.013	-0.005	39.916	-0.115	-0.115	0.000	0.000	0.000	0.000
27	A	32	GLN	0	-0.037	-0.023	42.209	-0.084	-0.084	0.000	0.000	0.000	0.000
28	A	33	GLN	0	-0.008	-0.011	42.284	-0.045	-0.045	0.000	0.000	0.000	0.000
29	A	34	ILE	0	-0.040	-0.017	41.369	-0.099	-0.099	0.000	0.000	0.000	0.000
30	A	35	ARG	1	1.001	0.995	44.806	-6.485	-6.485	0.000	0.000	0.000	0.000
31	A	36	ASP	-1	-0.850	-0.897	47.519	6.051	6.051	0.000	0.000	0.000	0.000
32	A	37	GLN	0	-0.055	-0.025	46.053	0.015	0.015	0.000	0.000	0.000	0.000
33	A	38	HIS	0	-0.056	-0.036	45.834	-0.150	-0.150	0.000	0.000	0.000	0.000
34	A	39	PRO	0	0.059	0.036	48.773	0.079	0.079	0.000	0.000	0.000	0.000
35	A	40	SER	0	-0.035	-0.009	51.298	0.029	0.029	0.000	0.000	0.000	0.000
36	A	41	LYS	1	0.833	0.909	46.170	-6.498	-6.498	0.000	0.000	0.000	0.000
37	A	42	ILE	0	0.078	0.045	43.443	0.035	0.035	0.000	0.000	0.000	0.000
38	A	43	PRO	0	-0.055	-0.013	40.817	0.142	0.142	0.000	0.000	0.000	0.000
39	A	44	VAL	0	0.025	-0.003	37.946	0.054	0.054	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.036	-0.009	32.917	0.176	0.176	0.000	0.000	0.000	0.000
41	A	46	ILE	0	-0.006	-0.009	33.371	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	47	GLU	-1	-0.841	-0.920	28.294	10.561	10.561	0.000	0.000	0.000	0.000
43	A	48	ARG	1	0.919	0.967	21.730	-12.632	-12.632	0.000	0.000	0.000	0.000
44	A	49	TYR	0	0.055	0.015	27.416	0.243	0.243	0.000	0.000	0.000	0.000
45	A	50	LYS	1	0.915	0.952	22.494	-11.915	-11.915	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.052	0.025	23.255	0.546	0.546	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.787	-0.872	24.312	10.928	10.928	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.807	0.885	20.016	-12.784	-12.784	0.000	0.000	0.000	0.000
49	A	54	GLN	0	-0.006	0.020	23.789	0.215	0.215	0.000	0.000	0.000	0.000
50	A	55	LEU	0	-0.037	-0.003	26.646	-0.099	-0.099	0.000	0.000	0.000	0.000
51	A	56	PRO	0	0.053	0.032	26.014	0.461	0.461	0.000	0.000	0.000	0.000
52	A	57	VAL	0	0.003	0.006	23.578	-0.319	-0.319	0.000	0.000	0.000	0.000
53	A	58	LEU	0	0.007	0.005	26.657	-0.125	-0.125	0.000	0.000	0.000	0.000
54	A	59	ASP	-1	-0.786	-0.850	28.366	9.528	9.528	0.000	0.000	0.000	0.000
55	A	60	LYS	1	0.810	0.913	29.761	-8.410	-8.410	0.000	0.000	0.000	0.000
56	A	61	THR	0	0.022	0.007	29.735	0.156	0.156	0.000	0.000	0.000	0.000
57	A	62	LYS	1	0.928	0.962	32.178	-8.662	-8.662	0.000	0.000	0.000	0.000
58	A	63	PHE	0	-0.017	-0.024	34.226	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	64	LEU	0	0.035	0.030	38.792	-0.042	-0.042	0.000	0.000	0.000	0.000
60	A	65	VAL	0	-0.019	-0.009	41.869	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	66	PRO	0	-0.006	0.003	44.543	-0.062	-0.062	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.809	-0.908	48.356	6.181	6.181	0.000	0.000	0.000	0.000
63	A	68	HIS	0	-0.003	-0.016	50.219	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.076	-0.018	45.999	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	70	ASN	0	0.019	0.003	48.372	0.018	0.018	0.000	0.000	0.000	0.000
66	A	71	MET	0	0.078	0.035	42.893	0.170	0.170	0.000	0.000	0.000	0.000
67	A	72	SER	0	0.020	0.019	44.024	0.169	0.169	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.880	-0.933	45.177	6.360	6.360	0.000	0.000	0.000	0.000
69	A	74	LEU	0	0.021	0.008	40.722	0.128	0.128	0.000	0.000	0.000	0.000
70	A	75	VAL	0	-0.002	-0.008	40.078	0.220	0.220	0.000	0.000	0.000	0.000
71	A	76	LYS	1	0.899	0.939	40.164	-6.510	-6.510	0.000	0.000	0.000	0.000
72	A	77	ILE	0	-0.039	-0.018	40.294	0.125	0.125	0.000	0.000	0.000	0.000
73	A	78	ILE	0	0.004	0.001	35.380	0.149	0.149	0.000	0.000	0.000	0.000
74	A	79	ARG	1	0.895	0.965	36.054	-7.851	-7.851	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.934	0.953	36.964	-7.036	-7.036	0.000	0.000	0.000	0.000
76	A	81	ARG	1	0.788	0.867	34.432	-8.600	-8.600	0.000	0.000	0.000	0.000
77	A	82	LEU	0	-0.016	-0.005	30.647	0.208	0.208	0.000	0.000	0.000	0.000
78	A	83	GLN	0	-0.061	-0.017	32.786	0.152	0.152	0.000	0.000	0.000	0.000
79	A	84	LEU	0	-0.013	0.011	32.194	0.145	0.145	0.000	0.000	0.000	0.000
80	A	85	ASN	0	0.029	0.013	34.298	-0.406	-0.406	0.000	0.000	0.000	0.000
81	A	86	PRO	0	0.006	-0.018	37.364	0.043	0.043	0.000	0.000	0.000	0.000
82	A	87	THR	0	0.017	-0.003	36.318	-0.100	-0.100	0.000	0.000	0.000	0.000
83	A	88	GLN	0	-0.055	-0.004	31.982	0.142	0.142	0.000	0.000	0.000	0.000
84	A	89	ALA	0	0.048	0.033	34.688	-0.241	-0.241	0.000	0.000	0.000	0.000
85	A	90	PHE	0	-0.014	-0.033	33.789	0.289	0.289	0.000	0.000	0.000	0.000
86	A	91	PHE	0	0.004	0.023	35.179	-0.276	-0.276	0.000	0.000	0.000	0.000
87	A	92	LEU	0	-0.016	-0.020	35.363	0.270	0.270	0.000	0.000	0.000	0.000
88	A	93	LEU	0	0.008	-0.005	34.435	-0.236	-0.236	0.000	0.000	0.000	0.000
89	A	94	VAL	0	0.027	0.002	37.045	0.176	0.176	0.000	0.000	0.000	0.000
90	A	95	ASN	0	-0.030	-0.023	38.220	0.077	0.077	0.000	0.000	0.000	0.000
91	A	96	GLN	0	-0.002	0.001	33.616	-0.039	-0.039	0.000	0.000	0.000	0.000
92	A	97	HIS	0	0.016	0.015	38.194	-0.212	-0.212	0.000	0.000	0.000	0.000
93	A	98	SER	0	0.013	0.003	40.242	0.099	0.099	0.000	0.000	0.000	0.000
94	A	99	MET	0	0.041	0.028	41.104	-0.244	-0.244	0.000	0.000	0.000	0.000
95	A	100	VAL	0	-0.080	-0.028	42.331	-0.131	-0.131	0.000	0.000	0.000	0.000
96	A	101	SER	0	0.011	-0.009	44.180	-0.117	-0.117	0.000	0.000	0.000	0.000
97	A	102	VAL	0	-0.018	0.011	46.219	-0.151	-0.151	0.000	0.000	0.000	0.000
98	A	103	SER	0	-0.046	-0.042	48.127	0.091	0.091	0.000	0.000	0.000	0.000
99	A	104	THR	0	0.035	0.016	49.829	-0.037	-0.037	0.000	0.000	0.000	0.000
100	A	105	PRO	0	0.056	0.034	49.447	0.152	0.152	0.000	0.000	0.000	0.000
101	A	106	ILE	0	0.005	-0.009	43.070	0.046	0.046	0.000	0.000	0.000	0.000
102	A	107	ALA	0	0.016	0.008	47.287	0.082	0.082	0.000	0.000	0.000	0.000
103	A	108	ASP	-1	-0.864	-0.932	49.687	5.809	5.809	0.000	0.000	0.000	0.000
104	A	109	ILE	0	-0.058	-0.027	44.544	0.035	0.035	0.000	0.000	0.000	0.000
105	A	110	TYR	0	-0.071	-0.049	43.521	0.058	0.058	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.827	-0.921	46.070	6.285	6.285	0.000	0.000	0.000	0.000
107	A	112	GLN	0	-0.079	-0.045	47.878	-0.048	-0.048	0.000	0.000	0.000	0.000
108	A	113	GLU	-1	-0.856	-0.930	42.610	7.007	7.007	0.000	0.000	0.000	0.000
109	A	114	LYS	1	0.695	0.872	41.893	-6.202	-6.202	0.000	0.000	0.000	0.000
110	A	115	ASP	-1	-0.798	-0.900	37.367	8.124	8.124	0.000	0.000	0.000	0.000
111	A	116	GLU	-1	-0.908	-0.951	39.712	7.293	7.293	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.758	-0.873	36.466	8.083	8.083	0.000	0.000	0.000	0.000
113	A	118	GLY	0	0.037	0.020	39.977	-0.053	-0.053	0.000	0.000	0.000	0.000
114	A	119	PHE	0	-0.029	-0.010	37.197	-0.060	-0.060	0.000	0.000	0.000	0.000
115	A	120	LEU	0	0.062	0.043	39.907	-0.024	-0.024	0.000	0.000	0.000	0.000
116	A	121	TYR	0	-0.089	-0.079	32.923	0.335	0.335	0.000	0.000	0.000	0.000
117	A	122	MET	0	-0.013	0.000	35.480	-0.117	-0.117	0.000	0.000	0.000	0.000
118	A	123	VAL	0	-0.005	0.003	30.523	0.311	0.311	0.000	0.000	0.000	0.000
119	A	124	TYR	0	-0.009	-0.017	29.004	-0.223	-0.223	0.000	0.000	0.000	0.000
120	A	125	ALA	0	-0.023	-0.026	30.593	0.436	0.436	0.000	0.000	0.000	0.000
121	A	126	SER	0	0.019	-0.005	29.881	-0.314	-0.314	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.026	-0.004	29.682	-0.141	-0.141	0.000	0.000	0.000	0.000
123	A	128	GLU	-1	-0.851	-0.942	34.147	7.620	7.620	0.000	0.000	0.000	0.000
124	A	129	THR	0	-0.033	-0.014	33.185	0.013	0.013	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLU)