FMO DATABASE

FMODB ID: 59LZZ

Calculation Name: 3DB5-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UKN5

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	131
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1113545.326678
FMO2-HF: Nuclear repulsion	1061258.773538
FMO2-HF: Total energy	-52286.553141
FMO2-MP2: Total energy	-52437.9395

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:3:ACE )

Summations of interaction energy for fragment #1(A:3:ACE )

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.
0.579	1.137	0	-0.273	-0.285	0.001

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.007

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].	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	5	VAL	0	0.000	0.009	3.848	0.453	1.011	-0.273	-0.285	0.001
4	A	6	THR	0	-0.010	-0.007	6.604	0.274	0.274	0.000	0.000	0.000
5	A	7	PHE	0	0.007	-0.012	9.186	0.024	0.024	0.000	0.000	0.000
6	A	8	VAL	0	0.000	-0.007	12.840	0.051	0.051	0.000	0.000	0.000
7	A	9	PRO	0	-0.040	-0.012	15.771	-0.001	-0.001	0.000	0.000	0.000
8	A	10	ASP	-1	-0.881	-0.929	19.104	-0.169	-0.169	0.000	0.000	0.000
9	A	11	THR	0	-0.043	-0.037	22.387	-0.002	-0.002	0.000	0.000	0.000
10	A	12	PRO	0	-0.028	-0.014	24.554	0.003	0.003	0.000	0.000	0.000
11	A	13	ILE	0	-0.011	0.001	27.200	0.008	0.008	0.000	0.000	0.000
12	A	14	GLU	-1	-0.928	-0.964	30.614	-0.064	-0.064	0.000	0.000	0.000
13	A	15	SER	0	0.001	-0.012	33.614	0.001	0.001	0.000	0.000	0.000
14	A	16	ARG	1	0.985	0.985	36.923	0.051	0.051	0.000	0.000	0.000
15	A	17	ALA	0	-0.019	0.004	39.549	0.002	0.002	0.000	0.000	0.000
16	A	18	ARG	1	0.852	0.887	36.804	0.057	0.057	0.000	0.000	0.000
17	A	19	LEU	0	-0.002	0.015	34.213	0.002	0.002	0.000	0.000	0.000
18	A	20	SER	0	-0.080	-0.040	38.383	0.003	0.003	0.000	0.000	0.000
19	A	21	LEU	0	-0.007	0.000	41.210	0.003	0.003	0.000	0.000	0.000
20	A	22	PRO	0	-0.007	-0.004	42.143	0.000	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.884	0.942	41.732	0.027	0.027	0.000	0.000	0.000
22	A	24	GLN	0	-0.012	-0.011	42.775	-0.001	-0.001	0.000	0.000	0.000
23	A	25	LEU	0	-0.016	-0.002	44.702	0.002	0.002	0.000	0.000	0.000
24	A	26	VAL	0	0.034	0.006	41.504	-0.002	-0.002	0.000	0.000	0.000
25	A	27	LEU	0	-0.027	0.002	39.924	0.001	0.001	0.000	0.000	0.000
26	A	28	ARG	1	0.958	0.972	41.095	0.026	0.026	0.000	0.000	0.000
27	A	29	GLN	0	-0.038	-0.001	43.072	-0.001	-0.001	0.000	0.000	0.000
28	A	30	SER	0	-0.061	-0.061	44.959	0.002	0.002	0.000	0.000	0.000
29	A	31	ILE	0	0.001	0.021	48.609	0.000	0.000	0.000	0.000	0.000
30	A	32	VAL	0	-0.104	-0.071	51.438	0.000	0.000	0.000	0.000	0.000
31	A	33	GLY	0	0.042	0.019	51.019	0.001	0.001	0.000	0.000	0.000
32	A	34	ALA	0	-0.038	-0.029	48.881	-0.001	-0.001	0.000	0.000	0.000
33	A	35	GLU	-1	-0.821	-0.920	45.580	-0.031	-0.031	0.000	0.000	0.000
34	A	36	VAL	0	-0.050	0.014	41.251	0.001	0.001	0.000	0.000	0.000
35	A	37	GLY	0	0.073	0.040	44.543	0.001	0.001	0.000	0.000	0.000
36	A	38	VAL	0	-0.015	-0.006	45.323	-0.001	-0.001	0.000	0.000	0.000
37	A	39	TRP	0	-0.035	-0.021	46.033	0.003	0.003	0.000	0.000	0.000
38	A	40	THR	0	-0.027	-0.023	46.681	-0.002	-0.002	0.000	0.000	0.000
39	A	41	GLY	0	0.039	0.026	45.269	0.000	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.863	-0.924	46.163	-0.023	-0.023	0.000	0.000	0.000
41	A	43	THR	0	0.003	-0.015	49.123	0.000	0.000	0.000	0.000	0.000
42	A	44	ILE	0	-0.027	-0.003	49.900	-0.001	-0.001	0.000	0.000	0.000
43	A	45	PRO	0	0.031	0.025	53.889	0.001	0.001	0.000	0.000	0.000
44	A	46	VAL	0	0.025	0.032	57.402	-0.001	-0.001	0.000	0.000	0.000
45	A	47	ARG	1	0.880	0.934	59.788	0.016	0.016	0.000	0.000	0.000
46	A	48	THR	0	0.026	0.032	53.622	0.000	0.000	0.000	0.000	0.000
47	A	49	CYS	0	-0.051	-0.034	56.331	0.000	0.000	0.000	0.000	0.000
48	A	50	PHE	0	0.036	0.018	50.325	-0.001	-0.001	0.000	0.000	0.000
49	A	51	GLY	0	0.011	0.015	51.913	0.001	0.001	0.000	0.000	0.000
50	A	52	PRO	0	0.006	-0.010	51.948	0.000	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.035	-0.043	50.511	-0.002	-0.002	0.000	0.000	0.000
52	A	54	ILE	0	-0.065	-0.023	46.915	0.000	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.039	-0.017	48.577	0.000	0.000	0.000	0.000	0.000
54	A	56	GLN	0	0.031	0.024	46.680	0.001	0.001	0.000	0.000	0.000
55	A	57	GLN	0	0.018	0.004	50.119	0.002	0.002	0.000	0.000	0.000
56	A	58	SER	0	0.011	-0.002	53.471	-0.001	-0.001	0.000	0.000	0.000
57	A	59	HIS	0	-0.019	-0.009	55.788	0.000	0.000	0.000	0.000	0.000
58	A	60	NME	0	0.007	0.024	59.370	0.000	0.000	0.000	0.000	0.000
59	A	70	ACE	0	0.048	0.013	52.208	0.000	0.000	0.000	0.000	0.000
60	A	71	VAL	0	0.007	-0.022	53.089	0.001	0.001	0.000	0.000	0.000
61	A	72	ASN	0	-0.031	-0.001	53.915	0.000	0.000	0.000	0.000	0.000
62	A	73	HIS	0	0.017	0.025	50.737	0.000	0.000	0.000	0.000	0.000
63	A	74	ILE	0	-0.012	-0.013	53.132	-0.001	-0.001	0.000	0.000	0.000
64	A	75	TRP	0	-0.020	0.000	53.369	0.002	0.002	0.000	0.000	0.000
65	A	76	LYS	1	0.956	0.976	57.641	0.023	0.023	0.000	0.000	0.000
66	A	77	ILE	0	0.014	0.017	58.286	0.001	0.001	0.000	0.000	0.000
67	A	78	TYR	0	-0.009	-0.019	61.593	0.000	0.000	0.000	0.000	0.000
68	A	79	HIS	0	0.014	0.010	64.836	0.000	0.000	0.000	0.000	0.000
69	A	80	ASN	0	-0.002	-0.011	66.814	0.000	0.000	0.000	0.000	0.000
70	A	81	GLY	0	-0.001	0.010	69.856	0.000	0.000	0.000	0.000	0.000
71	A	82	VAL	0	0.029	0.030	67.000	0.000	0.000	0.000	0.000	0.000
72	A	83	LEU	0	-0.066	-0.039	62.297	0.000	0.000	0.000	0.000	0.000
73	A	84	GLU	-1	-0.893	-0.952	62.643	-0.024	-0.024	0.000	0.000	0.000
74	A	85	PHE	0	-0.033	-0.028	56.586	-0.001	-0.001	0.000	0.000	0.000
75	A	86	CYS	0	-0.029	-0.013	57.340	0.001	0.001	0.000	0.000	0.000
76	A	87	ILE	0	0.002	0.018	52.354	-0.001	-0.001	0.000	0.000	0.000
77	A	88	ILE	0	0.012	0.004	50.109	0.001	0.001	0.000	0.000	0.000
78	A	89	THR	0	-0.042	-0.056	49.060	-0.001	-0.001	0.000	0.000	0.000
79	A	90	THR	0	0.061	0.024	46.647	0.001	0.001	0.000	0.000	0.000
80	A	91	ASP	-1	-0.813	-0.893	42.079	-0.056	-0.056	0.000	0.000	0.000
81	A	92	GLU	-1	-0.740	-0.864	39.170	-0.054	-0.054	0.000	0.000	0.000
82	A	93	ASN	0	-0.062	-0.035	37.885	-0.004	-0.004	0.000	0.000	0.000
83	A	94	GLU	-1	-0.945	-0.979	40.870	-0.048	-0.048	0.000	0.000	0.000
84	A	95	CYS	0	-0.091	-0.016	44.039	0.003	0.003	0.000	0.000	0.000
85	A	96	ASN	0	0.038	0.015	43.848	-0.002	-0.002	0.000	0.000	0.000
86	A	97	TRP	0	0.097	0.027	43.903	0.001	0.001	0.000	0.000	0.000
87	A	98	MET	0	-0.076	-0.007	45.190	0.001	0.001	0.000	0.000	0.000
88	A	99	MET	0	-0.030	-0.002	44.411	0.001	0.001	0.000	0.000	0.000
89	A	100	PHE	0	-0.025	-0.015	41.414	0.000	0.000	0.000	0.000	0.000
90	A	101	VAL	0	-0.068	-0.016	47.120	0.001	0.001	0.000	0.000	0.000
91	A	102	ARG	1	0.906	0.945	46.164	0.035	0.035	0.000	0.000	0.000
92	A	103	LYS	1	0.915	0.963	52.385	0.023	0.023	0.000	0.000	0.000
93	A	104	ALA	0	0.003	0.010	56.137	0.000	0.000	0.000	0.000	0.000
94	A	105	ARG	1	0.845	0.895	56.442	0.021	0.021	0.000	0.000	0.000
95	A	106	ASN	0	-0.037	-0.014	59.996	0.001	0.001	0.000	0.000	0.000
96	A	107	ARG	1	0.958	0.960	62.094	0.015	0.015	0.000	0.000	0.000
97	A	108	GLU	-1	-0.895	-0.943	62.852	-0.015	-0.015	0.000	0.000	0.000
98	A	109	GLU	-1	-0.818	-0.888	57.367	-0.020	-0.020	0.000	0.000	0.000
99	A	110	GLN	0	-0.036	-0.022	58.301	-0.001	-0.001	0.000	0.000	0.000
100	A	111	ASN	0	0.039	0.017	55.042	0.000	0.000	0.000	0.000	0.000
101	A	112	LEU	0	0.018	0.017	53.386	0.000	0.000	0.000	0.000	0.000
102	A	113	VAL	0	-0.025	-0.007	58.180	0.000	0.000	0.000	0.000	0.000
103	A	114	ALA	0	0.014	-0.001	57.806	-0.001	-0.001	0.000	0.000	0.000
104	A	115	TYR	0	-0.040	-0.038	59.431	0.001	0.001	0.000	0.000	0.000
105	A	116	PRO	0	0.027	0.007	60.175	-0.001	-0.001	0.000	0.000	0.000
106	A	117	HIS	0	-0.012	-0.013	60.658	0.001	0.001	0.000	0.000	0.000
107	A	118	ASP	-1	-0.877	-0.934	60.594	-0.023	-0.023	0.000	0.000	0.000
108	A	119	GLY	0	-0.008	-0.007	60.529	-0.001	-0.001	0.000	0.000	0.000
109	A	120	LYS	1	0.866	0.941	54.111	0.029	0.029	0.000	0.000	0.000
110	A	121	ILE	0	-0.004	0.010	55.676	0.001	0.001	0.000	0.000	0.000
111	A	122	PHE	0	0.048	0.025	55.461	-0.001	-0.001	0.000	0.000	0.000
112	A	123	PHE	0	-0.011	-0.006	52.054	0.001	0.001	0.000	0.000	0.000
113	A	124	CYS	0	-0.004	0.000	56.176	0.000	0.000	0.000	0.000	0.000
114	A	125	THR	0	-0.016	-0.019	55.643	0.000	0.000	0.000	0.000	0.000
115	A	126	SER	0	-0.035	-0.027	58.442	0.001	0.001	0.000	0.000	0.000
116	A	127	GLN	0	-0.047	-0.021	59.935	0.001	0.001	0.000	0.000	0.000
117	A	128	ASP	-1	-0.812	-0.917	58.313	-0.016	-0.016	0.000	0.000	0.000
118	A	129	ILE	0	-0.065	-0.023	53.693	0.000	0.000	0.000	0.000	0.000
119	A	130	PRO	0	0.005	0.003	54.226	0.000	0.000	0.000	0.000	0.000
120	A	131	PRO	0	0.048	0.036	49.171	-0.001	-0.001	0.000	0.000	0.000
121	A	132	GLU	-1	-0.925	-0.973	46.731	-0.021	-0.021	0.000	0.000	0.000
122	A	133	ASN	0	-0.093	-0.042	49.328	0.001	0.001	0.000	0.000	0.000
123	A	134	GLU	-1	-0.761	-0.856	49.819	-0.028	-0.028	0.000	0.000	0.000
124	A	135	LEU	0	-0.041	-0.028	50.288	0.001	0.001	0.000	0.000	0.000
125	A	136	LEU	0	0.007	0.004	52.480	-0.001	-0.001	0.000	0.000	0.000
126	A	137	PHE	0	0.001	0.013	54.459	0.001	0.001	0.000	0.000	0.000
127	A	138	TYR	0	-0.020	-0.026	57.320	0.000	0.000	0.000	0.000	0.000
128	A	139	TYR	0	0.020	0.034	58.857	0.000	0.000	0.000	0.000	0.000
129	A	140	SER	0	0.038	0.010	62.549	0.001	0.001	0.000	0.000	0.000
130	A	141	ARG	1	0.836	0.901	65.184	0.017	0.017	0.000	0.000	0.000
131	A	142	NME	0	0.050	0.043	68.763	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )