FMO DATABASE

FMODB ID: 3Q14L

Calculation Name: 3UEB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3UEB

Chain ID: A

ChEMBL ID:

UniProt ID: B6YTZ3

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-780298.362817
FMO2-HF: Nuclear repulsion	739359.92467
FMO2-HF: Total energy	-40938.438147
FMO2-MP2: Total energy	-41060.1027

3D Structure Molmil

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:4:GLY)

Summations of interaction energy for fragment #1(A:4:GLY)

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.
-1.123	0.919	-0.014	-0.896	-1.131	-0.001

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.010

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	6	SER	0	-0.005	0.002	3.578	-1.312	0.599	-0.013	-0.880	-1.018	-0.001
4	A	7	GLY	0	0.068	0.053	4.489	0.128	0.259	-0.001	-0.016	-0.113	0.000
5	A	8	LYS	1	0.849	0.917	6.992	-0.252	-0.252	0.000	0.000	0.000	0.000
6	A	9	ARG	1	0.849	0.909	10.428	-0.003	-0.003	0.000	0.000	0.000	0.000
7	A	10	VAL	0	0.026	0.011	13.336	0.007	0.007	0.000	0.000	0.000	0.000
8	A	11	ILE	0	-0.043	-0.005	16.978	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	12	HIS	0	-0.016	-0.008	19.813	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	13	ILE	0	0.025	-0.001	23.358	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	14	GLY	0	0.011	0.023	26.267	0.004	0.004	0.000	0.000	0.000	0.000
12	A	15	LEU	0	-0.034	-0.026	29.177	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	16	PRO	0	0.022	-0.006	32.481	0.000	0.000	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.981	-0.987	35.979	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.003	0.026	33.026	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	19	SER	0	0.013	0.014	36.957	0.003	0.003	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.885	-0.979	35.843	0.022	0.022	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.971	-0.978	35.238	0.007	0.007	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.073	0.021	35.286	0.000	0.000	0.000	0.000	0.000	0.000
20	A	23	LEU	0	-0.007	0.007	31.169	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	24	ILE	0	-0.022	-0.002	30.708	0.001	0.001	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.889	-0.936	30.471	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	26	ILE	0	-0.011	-0.008	28.255	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.001	-0.018	26.651	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.916	-0.981	25.682	0.005	0.005	0.000	0.000	0.000	0.000
26	A	29	LEU	0	0.007	0.017	26.188	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	30	ALA	0	-0.018	0.004	23.291	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	31	GLN	0	-0.027	-0.034	21.396	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.905	-0.963	21.185	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	33	THR	0	-0.033	-0.014	21.734	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	34	ILE	0	-0.048	-0.034	16.582	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.027	-0.014	17.872	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	36	ASP	-1	-0.895	-0.942	19.232	-0.078	-0.078	0.000	0.000	0.000	0.000
34	A	37	TYR	0	-0.051	-0.031	16.048	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	38	VAL	0	-0.012	0.002	13.981	-0.035	-0.035	0.000	0.000	0.000	0.000
36	A	39	PHE	0	-0.038	-0.031	16.139	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.934	-0.943	18.641	-0.112	-0.112	0.000	0.000	0.000	0.000
38	A	41	HIS	1	0.727	0.839	16.017	0.186	0.186	0.000	0.000	0.000	0.000
39	A	42	LEU	0	0.015	0.030	11.433	-0.059	-0.059	0.000	0.000	0.000	0.000
40	A	43	THR	0	-0.038	-0.003	15.722	0.061	0.061	0.000	0.000	0.000	0.000
41	A	44	ARG	1	1.008	0.974	16.354	0.070	0.070	0.000	0.000	0.000	0.000
42	A	45	SER	0	-0.050	-0.030	16.830	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.896	-0.958	12.367	-0.408	-0.408	0.000	0.000	0.000	0.000
44	A	47	VAL	0	0.007	0.014	11.747	-0.078	-0.078	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.833	0.925	10.056	-0.177	-0.177	0.000	0.000	0.000	0.000
46	A	49	ASP	-1	-0.888	-0.959	12.335	0.219	0.219	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.004	-0.002	12.488	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.947	-0.959	14.624	0.223	0.223	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.004	-0.008	15.893	0.004	0.004	0.000	0.000	0.000	0.000
50	A	53	THR	0	-0.011	0.004	18.409	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	54	MET	0	0.044	0.032	20.930	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.863	0.941	23.933	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	56	ILE	0	0.052	0.017	26.062	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	57	ASN	0	-0.088	-0.066	29.537	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.846	0.909	31.518	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	59	GLU	-1	-0.981	-0.982	33.828	0.030	0.030	0.000	0.000	0.000	0.000
57	A	60	GLU	-1	-0.963	-0.962	31.885	0.056	0.056	0.000	0.000	0.000	0.000
58	A	61	THR	0	-0.096	-0.054	27.785	0.005	0.005	0.000	0.000	0.000	0.000
59	A	62	LEU	0	-0.019	-0.023	26.683	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	63	ASP	-1	-0.744	-0.859	29.267	0.016	0.016	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.016	0.010	25.235	0.002	0.002	0.000	0.000	0.000	0.000
62	A	65	GLU	-1	-0.926	-0.964	22.752	0.078	0.078	0.000	0.000	0.000	0.000
63	A	66	ILE	0	0.012	0.005	18.835	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.915	-0.955	16.309	0.199	0.199	0.000	0.000	0.000	0.000
65	A	68	VAL	0	0.002	0.000	13.222	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	69	TYR	0	-0.056	-0.047	9.532	0.156	0.156	0.000	0.000	0.000	0.000
67	A	70	LEU	0	-0.009	0.003	9.509	-0.064	-0.064	0.000	0.000	0.000	0.000
68	A	71	GLU	-1	-0.851	-0.909	7.658	0.621	0.621	0.000	0.000	0.000	0.000
69	A	72	VAL	0	-0.006	0.001	6.358	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	73	PRO	0	-0.051	-0.037	7.827	0.089	0.089	0.000	0.000	0.000	0.000
71	A	74	ILE	0	0.038	0.006	6.313	-0.249	-0.249	0.000	0.000	0.000	0.000
72	A	75	PHE	0	-0.075	-0.028	7.122	-0.199	-0.199	0.000	0.000	0.000	0.000
73	A	76	VAL	0	-0.022	-0.005	8.674	0.098	0.098	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.897	0.944	6.845	0.246	0.246	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.061	0.025	6.573	0.294	0.294	0.000	0.000	0.000	0.000
76	A	79	ASP	-1	-0.946	-0.961	5.880	-1.359	-1.359	0.000	0.000	0.000	0.000
77	A	80	VAL	0	0.035	0.015	4.942	0.333	0.333	0.000	0.000	0.000	0.000
78	A	81	ASP	-1	-0.841	-0.919	5.812	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.918	0.991	7.882	0.539	0.539	0.000	0.000	0.000	0.000
80	A	83	LEU	0	-0.040	-0.021	9.720	0.084	0.084	0.000	0.000	0.000	0.000
81	A	84	ILE	0	-0.001	-0.002	9.258	0.088	0.088	0.000	0.000	0.000	0.000
82	A	85	ASP	-1	-0.855	-0.923	11.755	-0.109	-0.109	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.923	-0.974	13.772	-0.236	-0.236	0.000	0.000	0.000	0.000
84	A	87	ALA	0	-0.018	-0.004	15.058	0.026	0.026	0.000	0.000	0.000	0.000
85	A	88	VAL	0	-0.004	-0.004	15.540	0.025	0.025	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.937	-0.971	17.837	-0.051	-0.051	0.000	0.000	0.000	0.000
87	A	90	ARG	1	0.887	0.960	19.599	0.110	0.110	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.071	0.019	20.707	0.009	0.009	0.000	0.000	0.000	0.000
89	A	92	TYR	0	0.016	0.009	20.164	0.008	0.008	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.905	-0.933	24.035	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	94	ILE	0	-0.040	-0.030	24.342	0.003	0.003	0.000	0.000	0.000	0.000
92	A	95	VAL	0	0.048	0.019	25.764	0.004	0.004	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.899	-0.956	28.014	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.754	0.861	28.944	0.052	0.052	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.933	0.987	31.026	0.019	0.019	0.000	0.000	0.000	0.000
96	A	99	LEU	0	0.021	0.020	30.539	0.003	0.003	0.000	0.000	0.000	0.000
97	A	100	ARG	1	0.901	0.948	31.995	0.027	0.027	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.930	-0.956	35.704	-0.019	-0.019	0.000	0.000	0.000	0.000
99	A	102	ILE	0	0.029	0.000	34.987	0.001	0.001	0.000	0.000	0.000	0.000
100	A	103	ALA	0	-0.042	-0.018	38.083	0.001	0.001	0.000	0.000	0.000	0.000
101	A	104	ASN	0	-0.154	-0.078	39.928	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	105	GLU	-1	-1.007	-0.980	40.971	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)